Royal Netherlands Institute for Sea Research
Phone number
+31 (0)222 36 9534
Senior Scientist
  • Microbial Ecology and Evolution
  • Genomics & Transcriptomics
  • Bioinformatics
  • Extremophiles
  • Synthetic ecology

Dr. Henk Bolhuis

Senior Scientist

Bacteria at the base

Marine microbiologist Henk Bolhuis investigates the greenish-brown, slimy layers that cover parts of the beach and the mudflats at low tide. ‘Those are microbial mats. They consist of a wickerwork of algae and bacteria that is sometimes so strong you can even pull it off the floor as a tight mat. Our fundamental research into these microbes has revealed that bacteria play a role in coastal protection. They are currently being investigated for their use in the development of saline agriculture.’

Sticky mini solar panels

’We investigate cyanobacteria – blue-green algae – and diatoms, which are true algae. These are literally the mini solar panels and food factories of the mudflat and drive a rich community of hundreds of different species of bacteria. During the day, they use energy from sunlight to combine carbon dioxide with water to produce oxygen and sugars for growth and as a food reserve. They run on those sugars at night until the sun comes up again. This results in high biomass of microbes that form a rich food source for other lifeforms, such as shellfish.’

‘The excess sugars are excreted, as a result of which sand grains stick to each other. On the green beach of Schiermonnikoog, for example, you can see the consequences of that: the loose sand is held in place by the microbes, which provides plants with food and firm soil and resulted in a rich salt marsh vegetation. In that sense, microbes may form the basis for dune formation and natural coastal protection. Without these microbial mats, the sand would keep shifting.’

The beauty of microbes

‘My primary interest lies in the fundamental biology of these ecosystems. In fact, we can compare the five millimetres of microbial mats with the complete ocean ecosystem. It contains similar physical features in terms of light and oxygen gradients and a similar food web containing producers, predators and decomposers.’

‘Furthermore, I can really enjoy the beauty of microbes. An example is when filmmaker and photographer Wim van Egmond joins our team to make time-lapses of the undulating movements of microbes in the mudflat. Sooner or later, this type of research will eventually result in practical applications. For example, in the EU project SIMBA, we will investigate over the next few years whether salt-tolerant bacteria in the soil could be  key for making future farming more resilient to the intruding salinisation due to sea-level rise.’

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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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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 12 July 2024
Genetic insights shed light on shiny bacteria
Some bacteria form colonies that display striking, reflective colours. An international, interdisciplinary team with NIOZ researchers Henk Bolhuis and Bastiaan von Meijenfeldt, gained new genetic insights into the formation of such colours which…
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