Prof. dr. ir. Nico Boon

Telephone number: 
+32 9/264 59 76
Faculty staff


  • Master in Bio-engineer Cell and Gene Biotechnology; Ghent University; 1998
  • Ph.D. in Applied Biological Sciences; Ghent University; 2002

Professional activities

  • Head of the Department of Microbial and Biochemical Technology (Ghent University); 2011 – 2014; 2016 - 2017
  • Full Professor (Tenured; “Hoogleraar”) of Molecular Microbial Ecology (ZAP) at the Center for Microbial Ecology and Technology (Ghent University); 2014 – present
  • Associate Professor (Tenured; “Hoofddocent”) of Molecular Microbial Ecology (ZAP) at the Laboratory of Microbial Ecology and Technology (Ghent University); 2011 – 2014
  • Assistant Professor (Tenured; “Docent”) of Molecular Microbial Ecology (ZAP) at the Laboratory of Microbial Ecology and Technology (Ghent University); 2006 – 2011
  • FWO-post doc position awarded at the Laboratory of Microbial Ecology and Technology (Ghent University); 2006
  • Doctor-assistant position (AAP) at the Laboratory of Microbial Ecology and Technology (Ghent University); 2003 – 2006
  • Assistant position (AAP) at the Laboratory of Microbial Ecology and Technology (Ghent University); 2001 – 2003
  • Doctoral research at the project grant G.O.A. 12050797 of the "Ministerie van de Vlaamse Gemeenschap, Bestuur Wetenschappelijk Onderzoek" (Belgium); 1998 – 2001


Since 1998 the research has focused on the microbial ecology of soil, aquifer, aquaculture systems, drinking water and activated sludge systems. The areas of interests have been the development of molecular methods (Illumina sequencing, Denaturing Gradient Gel Electrophoresis, Fluorescent in situ Hybridisation, Real-Time PCR, Flow Cytometry, Raman spectroscopy) 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, the research interests are focussed on 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. At present, there is limited theoretical insight into the ecology of mixed microbial cultures and engineering practices to manage those microbial resources are fragmentary. The final aim is to structure and optimize the performance of the community with respect to a desirable set of outputs. This strategy is called Microbial Resource Management (MRM).

Research Leadership

Nico Boon is currently project promoter of a major national GOA project “Sustainable methanotrophs: from ecology to microbial resource management”. He is also involved in the ELECTRA project, an EU-China RTD joint initiative (2019-2022). He is a promoter or co-promoter of several national projects (FWO, Baekeland, …) dealing with the microbial ecology of different environments. Previously, he was the coordinator of the most important Belgian research program “Interuniversity Attraction Poles (IAP) Phase VII” of the Belgian Federal Science Policy Office (2012-2017) and coordinator of the FP7 ManureEcoMine. During his career, he participated as a partner or WP leader in more than 10 EU projects 

Publications and presentations

(Web of Science ResearcherIDGoogle ScholarOrcidUGent - academic library)

The research has resulted in more than 430 accepted/published international publications in journals with peer review. In 2018 he was taken up in the list of ISI Highly Cited Researchers. He published in top journals, like Nature, Nature Communications, FEMS Microbiology Reviews, Trends in Biotechnology, PLoS Pathogens, Plos One (6x), Current Opinion in Biotechnology (2x), Biotechnology Advances (2x), Trends in Biotechnology (3x), ISME Journal (5x)…They have been cited almost 18500 times with an h-index of 70. He has also seven patents. More than 30 international conferences have been attended, and the research results have been presented more than 80 national and international oral presentations.  

Teaching and supervision

Nico Boon was the supervisor of 50 finished PhD’s and is currently supervising 10 Ph.D.-students in microbial ecology and environmental engineering, and he has supervised more than 120 master students at Ghent University. He had within his group 15 postdocs at a junior or senior level. 
He coordinates several courses at the Bachelors and Masters level: Microbial Ecological Processes (since 2006), Molecular Microbial Techniques (2006-2014; 2016-now) and Environmental Microbiology (since 2011). At the faculty of Bioscience Engineering, he was the coordinator of the Master Bio-engineer Cell and Gene Biotechnology and was responsible for the restructuring of the Masters program (2009-2014). He has organized or co-organized more than 30 national and international workshops

Selected key publications: 
Wittebolle, L., M. Marzorati, L. Clement, A. Balloi, D. Daffonchio, K. Heylen, P. De Vos, W. Verstraete, and N. Boon. 2009. Initial community evenness favors functionality under selective stress. Nature 458:623-626.
De Roy, K., M. Marzorati, A. Negroni, O. Thas, A. Balloi, F. Fava, W. Verstraete, D. Daffonchio, and N. Boon. 2013. Invasion preserves functionality in uneven stressed communities. Nature Communications 4:1383
De Roy, K., L. Clement, O. Thas, Y. Y. Wang, and N. Boon. 2012. Flow cytometry for fast microbial community fingerprinting. Water Research 46:907-919.
Wang, Y., F. Hammes, K. De Roy, W. Verstraete, and N. Boon. 2010. Past, present and future applications of flow cytometry in aquatic microbiology. Trends in Biotechnology 28:416-424.
Boon, N., W. De Windt, W. Verstraete, and E. M. Top. 2002. Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiology Ecology 39:101-112.