Stijn van den Bergh

Stijn van den Bergh MSc

PhD Candidate


Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands



I want to contribute to a more sustainable world through my research on the interface of microbial ecology and sustainable agriculture.


After finishing my bachelor in Biology and master in Environmental Biology at Universiteit Utrecht, I started in January 2019 as a PhD candidate in the Microbial Ecology department at NIOO in the group of Paul Bodelier. My NWO-TTW Open Technology-funded project focuses on the occurrence and underlying mechanisms of organic residue-stimulated atmospheric methane uptake by agricultural soils.


Peer-reviewed publicaties

  • Soil Biology and Biochemistry

    Soil aggregate stability governs field greenhouse gas fluxes in agricultural soils

    Stijn van den Bergh, Iris Chardon, Marcio Fernandes Alves Leite, Gerard Korthals, Jochen Mayer, Mathias Cougnon, Dirk Reheul, Wietse de Boer, Paul Bodelier
    Agriculture is responsible for 30–50% of the yearly CO2, CH4, and N2O emissions. Soils have an important role in the production and consumption of these greenhouse gases (GHGs), with soil aggregates and the inhabiting microbes proposed to function as biogeochemical reactors, processing these gases. Here we studied, for the first time, the relationship between GHG fluxes and aggregate stability as determined via laser diffraction analysis (LDA) of agricultural soils, as well as the effect of sustainable agricultural management strategies thereon. Using the static chamber method, all soils were found to be sinks for CH4 and sources for CO2 and N2O. The application of organic amendments did not have a conclusive effect on soil GHG fluxes, but tilled soils emitted more CO2. LDA was a useful and improved method for assessing soil aggregate stability, as it allows for the determination of multiple classes of aggregates and their structural composition, thereby overcoming limitations of traditional wet sieving. Organic matter content was the main steering factor of aggregate stability. The presence of persistent stable aggregates and the disintegration coefficient of stable aggregates were improved in organic-amended and no-tilled soils. Predictive modelling showed that, especially in these soils, aggregate stability was a governing factor of GHG fluxes. Higher soil CH4 uptake rates were associated with higher aggregate stability, while CO2 and N2O emissions increased with higher aggregate stability. Altogether, it was shown that sustainable agricultural management strategies can be used to steer the soil's aggregate stability and, both consequently and outright, the soil GHG fluxes, thereby creating a potential to contribute to the mitigation of agricultural GHG emissions.
  • Waste Management

    The intrinsic methane mitigation potential and associated microbes add product value to compost

    Stijn van den Bergh, Iris Chardon, Marion Meima-Franke, Ohana Costa, Gerard Korthals, Wietse de Boer, Paul Bodelier
    Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 & ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h−1 g dw compost−1 and 25.19 ± 6.75 pmol h−1 g dw compost−1, respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.
  • Environmental Technology & Innovation

    Effect of pre-treatment processes of organic residues on soil aggregates

    Vania Scarlet Chavez-Rico, Stijn van den Bergh, Paul Bodelier, Miriam van Eekert, Yujia Luo, Klaas G.J. Nierop, Valentina Sechi, Adrie Veeken, Cees N.J. Buisman
    Process technologies, such as composting, anaerobic digestion, or lactic acid fermentation, greatly influence the resulting organic amendments (OAs) characteristics even when the same raw material is used. However, it is still unclear how these process technologies indirectly modify the effect of OAs on soil microbial activity and soil aggregation. To determine the effect of OA produced using pre-treatment technologies on the soil microbial activity and soil aggregation, we ran a soil column experiment in which we applied compost, digestate and lactic acid fermentation product made of the same model bio-waste. The results indicated that OAs produced under anaerobic conditions (fermented product and digestate) increased microbial activity, biomass, and soil micro- and macro-aggregation compared to compost and control treatments. Soil microbial activity strongly correlated to C, Ca, Mg, extracellular polymeric substances (EPS), fungal biomass, and macroaggregate formation (, ). Simultaneously, soil macroaggregate formation strongly correlated to water-extractable C, EPS, cation exchange capacity, K, Mg, Na, and bacterial biomass (, ). This study demonstrated that the effect of an organic substrate on soil properties can be modified towards desired effects using different pre-treatment technologies, suggesting the possibility of “engineer” OAs.

Projecten & samenwerkingen


  • SmartResidue

    Project 2019–2023
    This project will investigate residue-stimulated atmospheric methane oxidation, and aims to elucidate its occurrence in field conditions, responsible microorganisms, underlying mechanisms and controlling factors.
    Sampling compost