Current Research

Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. Thereby, microbes have a crucial role in many ecosystem services like provision of food, good climate as well clean water. However, our knowledge on how specific microbes, their traits and the functions they catalyse are connected to these ecosystem services is still rudimentary. In the Bodelier group we aim at connecting microbial identity to functioning in lab and field settings to elucidate the role of microbial diversity and traits in regulating important ecosystem processes like greenhouse gas emission from terrestrial and aquatic ecosystems. The work in our group links to the NIOO themes chemical communic​ation, microbiomes and global change.

Curriculum vitae (short version)

Education

MSc degree: Biology, Ecology and Microbiology (supervisors Prof. Dr. C.W.P.M. Blom and Prof. Dr. H.J. Laanbroek), University of Nijmegen, 1991.
PhD degree: Thesis: Nitrification and denitrification in the rhizosphere of Glyceria maxima: “The plant gives..the plant takes”.  (Promotors Prof. Dr. C.W.P.M. Blom and Prof. Dr. H.J. Laanbroek), University of Nijmegen, 1997.

Research Interests

Functional Ecology of microbial communities involved in biogeochemical cycles in terrestrial and aquatic ecosystems. The main research topics addressed are:

  • The role of microbial diversity, community composition and microbial traits in geochemical cycling.
  • The role of microbial diversity, community composition and traits in resistance and resilience against perturbations.
  • Impact of environmental drivers (e.g. agricultural practices, flooding, climate change, grazing etc.) on GHG fluxes from terrestrial and aquatic ecosystems.
  • Ecology of methane cycling microbes.
  • The importance of methane as energy source in aquatic foodwebs.
  • The exploitation of microbial communities for benefit of the society

Professional results

(Co) authorship of 100 papers in refereed journals of which 3 in Nature and 1 in PNAS, 7 book chapters, 1 Ebook, supervisor of 8completed PhD theses. H index = 38 (WOS), 46 (Google Scolar).  Researcher ID: http://www.researcherid.com/rid/A-9591-2011. Orcid: http://orcid.org/0000-0002-5757-5572

Academic functions

1991 – 1992        Research assistant, Netherlands Institute of Ecology, Centre for Terrestrial Ecology, Heteren, The Netherlands.

1992 – 1997        PhD student, Netherlands Institute of Ecology, Centre for Terrestrial Ecology (Heteren, The Netherlands).

1997 – 1999        Post-doctoral research fellow, Max-Planck Institute for Terrestrial Microbiology Marburg, Germany.

1999 – 2007        Post-doctoral research fellow, Netherlands Institute of Ecology, Centre for Limnology Nieuwersluis, the Netherlands.

2008 –                 Senior Researcher Netherlands Institute of Ecology, the Netherlands.

Editorial activities

  • Editorial board member of Applied and Environmental Microbiology 
  • Section Editor of Plant and Soil.
  • Editir in Chief Frontiers in Terrestrial Microbiology.
  • Editorial Board of the ISME Journal.

For an extended cv see 

Downloads

BE-Basic: Biogeochemical Indicator tools for assessing pollution of water bodies and sediments.
This project aims to develop monitoring tools to assess environmental impact invoked by bio-based agriculture, for example changes due to agricultural run-off in adjacent water bodies and sediments or exposure to pesticides. By screening a large set of ditches covering gradients in nutrient...Read more
BE-Basic SURESUPPORT. Towards a quick decision SUPPORT tool for SUstainable use of harvest RESidues.
Worldwide, erosion of agricultural soils is a very serious issue leading to loss of organic matter (OM) and associated soil functions leading to lower crop yields. However, soil quality and soil organic matter levels have to be secured which may be achieved through returning biomass from residues...Read more
LifeMOB: Unraveling of Life Strategies and Traits of Methane-Oxidizing Bacteria using a proteomic approach.
The dynamics of different groups of methane-oxidizing bacteria (MOB) are central to predicting variability in methane emissions, yet their quantitative responses to environmental conditions are still poorly understood. Here, we hypothesize that methane concentration, nitrogen and phosphorus...Read more
CCC: Clever Cover cropping. Synergistic Mixtures for Sustainable Soils
Since recently, Dutch farmers are required to grow cover crops in mixtures of at least two plant species. Cleverly chosen species mixtures can support greater inputs into the soil C reservoir, driving increases in soil N and P, and reduce pathogen pressure on the main crop. In this project we will...Read more
Icelandic grassland soils dominated by ammonia-oxidizing archaea, or not?
In the nitrogen-limited soils of Grændalur valley on Iceland, thaumarchaea dominated the process of ammonia oxidation. Ammonia-oxidizing betaproteobacteria came only to the fore in microcosms after addition of ammonium. Since this nitrogen-limited situation in the field might be due to the...Read more
The zooplankton-microbiome (MicroZoo): beyond microbe-host associations
Zooplankton is a crucial component of aquatic food webs. Microbes colonizing zooplankton species have been proposed to provide numerous ecosystem services including nutrient acquisition, stress protection, detoxification, and habitat provision but can also affect lake biogeochemistry by catalyzing...Read more
VolMob: Interactions between methanotrophs and heterotrophs mediated by volatile compounds
Methanotrophic bacteria are crucial in the regulation of methane concentration in the atmosphere and therefore for regulating our climate. Despite all research efforts there is still little understanding of the role of biological interaction on the functioning of methane oxidizers. In the VolMob...Read more
SmartResidue
Methane is a potent greenhouse gas and accounts for up to 17% of global warming according to the IPCC. Agricultural soils have always been regarded as a methane source, but recent research by the Bodelier group has shown that in laboratory conditions, these soils are capable of (circum-)atmospheric...Read more

Running projects

Functional Ecology of methane oxidizing bacteria

Methane oxidizing bacteria (MOB) utilize methane as their carbon and energy source. They perform this process in many ecosystems (soils, sediments lakes, permafrost etc) thereby reducing the emission of this greenhouse gas to the atmosphere. We study MOB in the lab as well as in the field. One of the most recent findings was the strong positive stimulation of MOB by other non-methanotrophic bacteria mediated by volatile compounds. We used special incubations chambers and a volatolomics approach to perform these confrontation assays. We are performing experiments to verify mechanisms of these interactions, but results indicate an as yet unexplored mechanisms of control of major biogeochemical cycles.

Microbiomes of Zooplankton   

Zooplankton is a crucial component of aquatic food webs. It is essential for keeping the water column clear, which is important for the presence of aquatic plants and animals. Like plants and higher animals, zooplankton hosts a rich community of microbes. Colonization of zooplankton species by microbes has been proposed to provide numerous ecosystem services including nutrient acquisition, stress protection, detoxification, and habitat provision. Next to this, the provision of a “sessile” mode of life of microbes on zooplankton surfaces may affect lake biogeochemistry by catalyzing important biogeochemical reactions (i.e. DOC conversions, methane production and consumption, nitrogen fixation, assimilating ammonia and phosphorus). In a project funded by the NIOO strategic fund, we combine forces with the department of Aquatic Ecology to explore the microbiomes of Zooplankton and its role for functioning of the animals as well as for aquatic biogeochemistry. Exploring of Polish lakes, a long-term mesocsosm experiment in Denmark as well as chemostat experiments performed at NIOO, it is already obviously that zooplankton species contain a very specific microbiome, very different from the surrounding water. Future experiments focus on elucidating the mechanisms and functional implications of these differences.

Smart residue applications to minimize GHG emissions from agricultural soils

Agriculture is one of the most important sources of the greenhouse gasses methane and nitrous oxide. To make agriculture more sustainable, emission shave to be reduced and soil degradation, loss of biodiversity and inefficient nutrient use has to be improved. We demonstrated that application of organic residues improved uptake of methane by agricultural soils, turning these soils even into sinks of GHG. In 3 projects we develop strategies to improve the GHG balance of agricultural soils by applying mixes of organic and mineral bio-based residues (financed by the Deutsche Forschungs Gesellschaft, DFG), by using mixes of cover crops to improve soil quality (Netherlands Organization for Scientific Research, NWO) and by using compost to improve uptake of atmospheric methane by agricultural soils (NWO-TTW, Smartresidue). 

 

Running projects

Functional Ecology of methane oxidizing bacteria

Methane oxidizing bacteria (MOB) utilize methane as their carbon and energy source. They perform this process in many ecosystems (soils, sediments lakes, permafrost etc) thereby reducing the emission of this greenhouse gas to the atmosphere. We study MOB in the lab as well as in the field. One of the most recent findings was the strong positive stimulation of MOB by other non-methanotrophic bacteria mediated by volatile compounds. We used special incubations chambers and a volatolomics approach to perform these confrontation assays. We are performing experiments to verify mechanisms of these interactions, but results indicate an as yet unexplored mechanisms of control of major biogeochemical cycles.

Microbiomes of Zooplankton   

Zooplankton is a crucial component of aquatic food webs. It is essential for keeping the water column clear, which is important for the presence of aquatic plants and animals. Like plants and higher animals, zooplankton hosts a rich community of microbes. Colonization of zooplankton species by microbes has been proposed to provide numerous ecosystem services including nutrient acquisition, stress protection, detoxification, and habitat provision. Next to this, the provision of a “sessile” mode of life of microbes on zooplankton surfaces may affect lake biogeochemistry by catalyzing important biogeochemical reactions (i.e. DOC conversions, methane production and consumption, nitrogen fixation, assimilating ammonia and phosphorus). In a project funded by the NIOO strategic fund, we combine forces with the department of Aquatic Ecology to explore the microbiomes of Zooplankton and its role for functioning of the animals as well as for aquatic biogeochemistry. Exploring of Polish lakes, a long-term mesocsosm experiment in Denmark as well as chemostat experiments performed at NIOO, it is already obviously that zooplankton species contain a very specific microbiome, very different from the surrounding water. Future experiments focus on elucidating the mechanisms and functional implications of these differences.

Smart residue applications to minimize GHG emissions from agricultural soils

Agriculture is one of the most important sources of the greenhouse gasses methane and nitrous oxide. To make agriculture more sustainable, emission shave to be reduced and soil degradation, loss of biodiversity and inefficient nutrient use has to be improved. We demonstrated that application of organic residues improved uptake of methane by agricultural soils, turning these soils even into sinks of GHG. In 3 projects we develop strategies to improve the GHG balance of agricultural soils by applying mixes of organic and mineral bio-based residues (financed by the Deutsche Forschungs Gesellschaft, DFG), by using mixes of cover crops to improve soil quality (Netherlands Organization for Scientific Research, NWO) and by using compost to improve uptake of atmospheric methane by agricultural soils (NWO-TTW, Smartresidue). 

 

Collaborations

 

National

 

 

International