Bodelier Group

Rationale

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 communication, microbiomes and global change.

Approach

We combine classical, genomic, isotopic and biogeochemical approaches to link communities to ecosystem fluxes and to assess distribution, functioning and controls of microbes in various habitats (e.g. floodplains, ditches, lakes, peatlands, and agricultural soils). Besides basic ecological questions we also explore the use of microbial functional groups and genes for the benefit of society e.g. as biogeochemical indicators of environmental disturbance by eutrophication or land use change or to optimize fertilizer strategies in agricultural soils minimizing greenhouse gas emissions.

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 2 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) and by using mixes of cover crops to improve soil quality (Netherlands Organization for Scientific Research , NWO).