Research groups

P1 and main co-ordinator

Prof. Nico Boon (LabMET, Ghent University, Belgium).

Since 1998, Prof. Boon’s research focused on the microbial ecology of soil, aquifer, aquaculture systems, drinking water, microbial fuel cells, gastrointestinal ecosystems, and activated sludge systems. The areas of interests have been the development of molecular methods (Denaturing Gradient Gel Electrophoresis, Fluorescent in situ Hybridisation, Real-Time PCR and Flow Cytometry) for the qualitative and quantitative description of microorganisms and investigations of microbial processes in carbon and nitrogen cycling, novel bioaugmentation strategies for xenobiotics, and the bioprecipitation and application of catalytic particles (Pd, Mn, Au and Ag). During the last years, his research interests include the development of new microbial ecological theories to link the microbial community structure to functionality. The central theme of this research is to understand the composition, functionality and the limits under which a microbial community can (optimally) perform. The final aim is to structure and optimize the performance of the community in respect to a desirable set of outputs. This strategy is called Microbial Resource Management (MRM).

Website : link

Prof. Bernard De Baets (Ghent University, Belgium)

Bernard De Baets is a Professor at the Department of Mathematical Modelling, Statistics and Bioinformation in Ghent University, and heads the KERMIT research unit on ‘Knowledge-based Systems’.

Website: link


Prof. Spiros Agathos (Université Catholique de Louvain, Belgium).

Spiros Agathos is professor at Université Catholique de Louvain (UCL) in Louvain-la-Neuve, within the Bioengineering Group (GEBI) of its Earth and Life Institute (ELI). He has a longstanding experience with biodegradation, bioprocess design and modelling. Before coming to Belgium in 1993, he had obtained his Ph.D. at MIT and served in professorial positions at the University of Western Ontario (Canada) and at Rutgers, the State University of New Jersey (USA). Over the last two decades, his group focused on bioconversions catalysed by pure strains or microbial communities for pollution control, bioenergy conversion, and value-added product formation. The breakdown of xenobiotics is studied from the single cell level (catabolic pathways) to the field scale (in situ bioremediation), where microbial diversity and functions in soils and aquifers (polluted and pristine) are monitored and characterized with molecular and eco-genomic techniques. This research is reinforced by the activities of Patrick Gerin’s team which studies microbial communities involved in anaerobic bioconversion of complex (biomass) substrates, in order to redirect their metabolism towards useful products (volatile fatty acids (VFA), alcohols, H2, CH4). Laboratory facilities include analytical equipment (HPLC, GC, spectro(fluori)metry, etc.), instrumented bioreactors including soil micro- and mesocosms, and biomolecular capabilities (PCR, DGGE, etc.).

Website : link


Prof. Dirk Springael (Katholieke Universiteit Leuven, Belgium)

Prof. Dirk Springael was appointed professor at the Catholic University of Leuven (KULeuven) in 2002 where he joined the Division of Soil and Water Management of the Faculty of Bioscience Engineering. He performs research on the microbial ecology of polluted soils and waters, and the microbiology and genetics of organic xenobiotic degrading bacteria. The research involves both fundamental and applied aspects. Emphasis of the fundamental research is on the genetic adaptation mechanisms involved in bacterial degradation of xenobiotics, genetics and physiology of interactions within pollutant degrading microbial consortia in biofilms and of interactions between pollutant degraders and others, and the study of the effects of the environment and disturbances on the microbial ecology of pollutant removing ecosystems. Applied research is on drinkingwater and wastewater purification systems and soil remediation. Target xenobiotic pollutants are pesticides, polycyclic aromatic hydrocarbons and VOCLs. The lab is fully equipped for performing microbiology and molecular biology. Expertises and methodologies used include genetics like mutagenesis, IVET technology, transcriptomics (micro-array analysis), biofilm operation, nucleic acid fingerprinting techniques, CLSM, FISH, PCR and real-time PCR, HPLC, UPLC, ICP-OES, DOC analysis and others.

Website : link


Prof. Ruddy Wattiez (Université de Mons, Belgium).

Prof. Ruddy Wattiez has built expertise in biochemistry and proteomics associated to microbiology since his thesis. In 2008, Prof R. Wattiez was appointed head of the ProtMic Lab. Since then, Ruddy Wattiez is developing his group devoted to biochemistry associated to microbiology with a special interest for environmental microbiology. We have developed proteomic approaches to study microbial proteomes from bacteria to viruses including metaproteomics. Our functional proteomic platform dedicated to microbiology features 5 mass spectrometers (5 mass spectrometers with HPLC/UPLC) as well as various molecular biology instruments (quantitative PCR, DGGE, etc.). In this context, he obtained in 2011 funds for a new high resolution mass spectrometer (Triple –tof ABSCIEX) dedicated to microbial quantitative proteomics. Thanks to its expertise, the lab is an active member of the MELISSA (Micro- Ecological Life Support System Alternative) group of European Space Agency and especially for the studies of bacteria stress. His group has 5 PhD theses since 2008. Our researches in microbial ecology were reinforced by the recent nomination of a new professor/researcher - David Gillan. Today, the group performs research on the microbial ecology of polluted soils and the microbiology and organic solvent degrading bacteria.

Website : link


Dr. Frederik Hammes (Swiss Federal Institute for Aquatic Science and Technology, Switzerland).

The Eawag Drinking Water Microbiology group has specific skills in analysis of indigenous bacteria on single cell level with flow cytometry (FCM), online FCM and real-time FCM, as well as real time microscopy. Additionally, the group has expertise in microbial growth and competition at low nutrient and cell concentrations, as found in drinking water environments.

Website : link


Prof. Barth Smets (Technical University of Denmark, Denmark).

Advanced confocal microscopic analysis of microbial populations and communities, biofilm cultivation and inspection, micrographic image analysis, micromanipulation, microelectrode measurements in biofilms, cultivation of bacteria under defined matric stress, bioreactor automation, instrumentation, experimental design for biokinetic parameter estimation, agent based and continuum modelling of microbial processes and interactions, bioreporter construction, microarray based transcriptome analysis, biofilm compositional analysis.

Website : link


Prof. Søren J. Sørensen (University of Copenhagen, Denmark).

Molecular methods in microbiology, High throughput sequencing and data analysis.     Transcriptomics, 16s and amplicon sequencing and deep genome sequencing. Gradient (rt) PCR, DGGE pulse-field electrophoresis. DNA-micro-array technology. Fluorometeric methods. Fluorescent microscopy FISH, FACS. Biosensors. Pioneering of new molecular methods and their applications. Søren Sørensen has a well-established national and international scientific network and an excellent track record for attracting and coordinating large-scale funding and multidisciplinary research projects. Søren Sorensen is director of the Large Scale Genome sequencing centre that houses the largest collection of state of the art sequencing equipment in Scandinavia.

Website : link