Brief summary of my research
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 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 firmly 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 behaviour in nature.
In my research I have focused on the microbial sulfur cycle, and in particular on sulfur bacteria that are present in natural ecosystems (e.g., soda lakes and stratified lakes) as well as in man-made ecosystems, such as full-scale bioreactors removing toxic sulfur compounds from wastewater. For this, I am using a systems biology approach in which I combine experimental work, state-of-the-art omics techniques, and mathematical modelling. With my appointment at the University of Amsterdam in 2011, I started to work on host-microbe interactions in seagrasses, sponges, and recently algae, i.e., the brown alga Sargassum and the green alga Caulerpa. In this research, I am looking at both the host and its microbiome, i.e., the holobiont, to obtain a comprehensive understanding of the role of the microbiome in the growth, development, and ecological success of the host.
International visibility, activities, awards, etc.
I am one of the leading experts in Microbial Ecology. I have worked at several universities and different research institutions, including the prestigious Max Planck Institute for Marine Microbiology in Germany. Parallel to these positions, I was a visiting scientist at the Netherlands Institute for Ecology (NIOO), and at the Joint Genome Institute (JGI, USA), and a visiting Professor at the University of Milan (Italy). Since 2011, I am a Professor in Microbial Systems Ecology at the University of Amsterdam and the coordinator of the Research Priority Area ‘Systems Biology’ at the University of Amsterdam (SysBA; (www.systemsbiology.amsterdam). SysBA is one of the twenty research areas of the University of Amsterdam that are regarded as the very best the UvA has to offer in research. It bridges two research institutes at the Faculty of Science, i.e., the Swammerdam Institute for Life Sciences (SILS) and the Institute for Biodiversity and Ecosystem Dynamics (IBED) and is funded by a core grant from the University of Amsterdam, the Faculty of Science, the participating institutes and by grants to its PIs. Research within SysBA is focusing on host-microbe interactions in humans, plants and other organisms.
During my career, I have supervised more than 35 PhD-students and 25 postdocs. Together with them, I published more than 261 publications, including papers in prestigious journals such as Nature, Nature Communications, Nature Reviews Microbiology, Science, PNAS, and Microbiome. My publications have been cited more than 30,028 times, resulting in an H-index of 72 (Web of Science, August 2021). A complete list of my publications can be found on my ORCID: https://orcid.org/0000-0002-2422-0732. In 2012, I obtained a prestigious ERC Advanced Grant of 2.2M€ to work on the microbial sulfur cycle in soda lakes. In this project, I used a systems biology approach 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. In addition, I obtained several other grants, including a 1M€ grant from the University of Amsterdam to continue the RPA Systems Biology. Because of my positions at different universities and research institutions, I have cooperated with many scientists worldwide on both curiosity and society-driven projects.
I organized several scientific meetings, including the prestigious Gordon Research Conference on Environmental and Applied Microbiology in 2003 and 2005 and the EMBO workshop on Microbial Sulfur Metabolism in 2012. From 2006-2009, I was the leader of the program on Novel Feedstocks within B-BASIC (Bio-Based Sustainable Industrial Chemistry, a consortium of universities, research institutions, and industrial companies. The complete B-BASIC consortium had a budget of 50 M€ and consisted of 15 postdocs and 40 PhD-students.
I was a member of the editorial board of different journals and Editor Mini-Reviews of FEMS Microbiology Ecology. Currently, I am in the editorial board of the journal Microbial Ecology and Associate Editor of the journal Microbiome. Moreover, I am a board member of the Division Microbial Ecology of the Dutch Society of Microbiology (KNVM). So, due to the different positions and activities, I created a broad international network of scientists working in different scientific disciplines.
Research interests: algal genomics, climate change, ecology, evolution, holobiont, hologenome, macroalgae, marine biology, marine microbiology, mathematic modelling, metabolic modelling, meta-omics, microbiology, microbial ecology, molecular biology, seagrasses, seaweed, soda lakes, stable isotope probing, sulfur bacteria, system biology