Eco-evolutionary dynamics in natural and laboratory ecosystems

I use various natural microbial ecosystems, both in field and laboratory settings, for experimental study on fundamental concepts of ecology and evolution.


A community can adapt to an altered environment by adjustment of relative species abundances through the process of species sorting (ecology) and may adapt by spontaneous mutations spreading in individual species (evolution) - with the relative importance gradually shifting from ecology to evolution over time. These processes are traditionally studied in isolation, growing evidence urges us to consider ecology and evolution simultaneously for understanding adaptive responses to change. We aim to establish an experimental system using a defined microbial community and serially propagate it in a novel environment to test how and when ecological and evolutionary changes (co)occur. 

Project description

We use experimental approaches with microbial ecosystems taken from traditional fermentation and also in communities of fungi. Traditional fermentation covers various indigenous fermented foods from Zambia, Zimbabwe, Benin, Bangladesh and wine from Flevoland. Fungal communities concern Aspergillus fumigatus in decaying plant material. We ask how environmental selection pressures such as processing method, temperature, use of fungicides and exposure to invaders affect microbial species dynamics both in the short (ecological timescale) and long term (evolutionary timescale). We use conventional microbial culturing techniques as well as amplicon sequencing and metagenomics.  


We have found that ecological selection pressures leads to shifts in microbial population structure that is repeatable when using different replicate communities. We find similar patters when using laboratory and field experiments.  

From this, we developed a concept that we would like to peruse further, asking at what timescales and by what types of (repeatable) changes microbial communities adapt. 

Further, we have developed an interdisciplinary project embedding questions on traditional fermentation to not only ecology and evolution, but also to food technology, human nutrition and entrepreneurship.