Royal Netherlands Institute for Sea Research
Royal Netherlands
Institute for Sea Research
Phone number
+31 (0)222 369 534
Senior Scientist
  • Microbial Ecology and Evolution
  • Genomics & Transcriptomics
  • Bioinformatics
  • Extremophiles
  • Synthetic ecology

Dr. Henk Bolhuis

Senior Scientist

Research interests

  1. Molecular ecology and evolution of complex natural marine microbial ecosystems using in depth analysis of DNA (metagenomics) and RNA (metatranscriptomics).
  2. Synthetic ecology: through the use of synthetic microbial communities, bacterial consortia growing under near natural conditions, allow me to study microbial interactions of various complexity under controlled conditions. 
  3. Long term community evolution of assamblages of naturally  co-occuring microbial species from different domains of life.
  4. Establishing insight in the mechanisms of evolution and genetic change in Archaea with emphasis on halophilic Archaea.
  5. Environmental microbiology: Polar regions, hypersaline ecosystems and microbial mats.

Minimal Microbial Mats

Synthetic Microbial Ecology (Minimal Microbial Mats) 


Student Projects

MAIL me for student projects in bioinformatics, extremophiles and marine microbial ecology.


  • Masters Degree in Molecular Biology. University of Groningen (1990)
  • PhD degree:  Molecular Microbiology. Thesis: Multidrug Resistance in Lactococcus lactis  (advisors Prof. W.N. Konings, Prof. A.J.M. Driessen, Prof B. Poolman), University of Groningen, 1996 (Cum laude; upper 5%           

Former appointments

  • Senior Scientist, Marine Microbiology, NIOO-CEME, Yerseke (2006-2012)
  • Post Doctoral researcher, Microbial Ecology & Marine Biology, University of Groningen (2002-2006)
  • Assistant Professor (UD), Microbial Ecology, UNiversity of Groningen (2000-2002)
  • Post Doctoral researcher, Microbial Ecology, University of Groningen (1998-2000)
  • HFSPO Research fellow,  Max Planck Institute for  Biochemistry, Martinsried, Germany.

Professional results

  • (Co)authorship of over 50 publications, >3000 citations, 1 Nature, 1 Science, 2 PNAS, 1 EMBO J.
  • Current Hirsh index 25 (google citations)
  • Co-advisor of 4 PhD students, 3 planned 2017-2018

Prizes and awards

  • 1996 Max Gruber Award for best 1st scientific Ph.D. publication at University of Groningen
  • 1996 RUG/SNS-bank Dissertation Award for best Ph.D. thesis, Natural studies at University of Groningen period 1992-1996. 
  • 1996 Fellowship from the Human frontier Science Programme Organization (HFSPO) for a post doctoral position at the Max Planck Institute for Biochemistry, Munich, Germany. Project; Structure  function analysis of the sensory-rhodopsin I complex from Halobacterium salinarum.  

Selected Key publications

  • Hörnlein, C.; Confurius-Guns, V.; Stal, L.J.; Bolhuis, H. (2018). Daily rhythmicity in coastal microbial mats. npj Biofilms and Microbiomes 4: 11.
  • Bolhuis H, Martin-Cuadrado AB, Rosselli R, Pasic L & Rodriguez-Valera F (2017) Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface. BMC Genomics 18.
  • Bolhuis, H., and Stal, L.J. (2011) Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing. ISME J. 5, 1701-1712.
  • Bolhuis, H., Palm, P., Wende, A., Falb, M., Rampp, M., Rodriguez-Valera, F., Pfeiffer, F. and Oesterhelt, D. (2006). The genome of the square archaeon “Haloquadratum walsbyi”: life at the limits of water activity. BMC genomics 7, 169.
  • Daffonchio, D., S. Borin, T. Brusa, L.Brusetti, P. W. J. J. van der Wielen, H. Bolhuis, M. M. Yakimov, G. D’Auria, L. Giuliano, D. Marty, C. Tamburini, T. J. McGenity, J. E. Hallsworth, A. M. Sass, K. N. Timmis, A. Tselepides, G. J. de Lange, A.Hubner, J. Thomson, S. P. Varnavas, F. Gasparoni, H. W. Gerber, E. Malinverno, C. Corselli & Biodeep Scientific Party (2006) Stratified prokaryote network in the oxic–anoxic transition of a deep-sea halocline. Nature 440, 203-207.
  • Wielen van der, P.W. J., H. Bolhuis et al. (2005) The Enigma of Prokaryotic Life in Deep Hypersaline Anoxic Basins, Science 307, 121-123. 
  • Bolhuis,H., Te Poele. E.M. and Rodrigues-Valera, F.E. (2004) Isolation and cultivation of Walsby’s Square Archaeon. Environ. Microbiol. 6, 1287-1291.
  • Bolhuis,H., van Veen,H.W., Molenaar,D., Poolman,B., Driessen,A.J.M. and Konings,W.N. (1996) Multidrug resistance in Lactococcus lactis: Evidence for ATPdependent drug extrusion from the inner leaflet of the cytoplasmic membrane. the EMBO journal., 15, 4239-4245. 

Contact me!

Phone: +31 0222-369-534



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Citations on Google Scholar

Fieldwork at Schiermonnikoog

Students working on coastal microbial mats at Schiermonnikoog, the Netherlands

Hip to be Square

Haloquadratum walsbyi (Strain HBSQ001) the enigmatic square hyperhalophilic Archaeon 


DNA laboratory in Brunei

Linked news

Friday 21 February 2020
Launch of the Marine Microbiome Roadmap
In Brussels on 5th February at a meeting of the AORA Marine Microbiome group at the Skeikampen, Thon Hotel Brussels City Centre the AORA Marine Microbiome Roadmap has been launched. NIOZ researcher Henk Bolhuis joined the team who put this together.…
Tuesday 15 May 2018
Algenmatten met een biologische klok – een natuurlijke kustbescherming
De stijgende zeespiegel en harde winden bedreigen onze Noordzeestranden en laten veel zand in de zee verdwijnen. Maar op Schiermonnikoog hebben ze dit probleem niet, door clusters van minuscule algen en bacteriën die als een soort microbiële matten…
Thursday 01 June 2017
Tijdschrift special over Nederlands Antarctisch Onderzoek
Het Dirck Gerritsz laboratorium is het eerste Nederlandse laboratorium op Antarctica. Het werd in januari 2013 feestelijk geopend door het Ministerie van OCW, als resultaat van goede samenwerking met de British Antarctic Survey (BAS). Na vier jaar…

NIOZ publications

Linked projects

POMVIDDY_Polar marine diversity and dynamics
Corina Brussaard
Netherlands Organization for Scientific Research
Project duration
23 May 2017 - 22 May 2021
Metabolic Networks
Henk Bolhuis
Netherlands Organization for Scientific Research
Project duration
31 Dec 2011 - 16 Jul 2017