Ecology & Evolution and Systems Ecology have four main research themes

1 – Climate change and ecosystem functioning

Climate change strongly affects the interactions between vegetation, fauna, soil, hydrosphere and atmosphere and has a strong impact on biodiversity. In this research theme we investigate these interactions using a systems ecological approach with ramifications to soil microbial ecology and paying particular attention to feedback mechanisms. We use functional traits as the basis for response and effect parameters. The research is performed at the full array of hierarchical levels, going from soil microbial ecology to global scale vegetation- and biogeochemical models and our study sites range from Arctic tundra to tropical rain forest.


  • HoliSoils [Luyssaert, Naudts, Jeong, Cornelissen, Berg, Guenet, Yueste, Flores, Schelhaas, Nabuurs]
    Using the ORCHIDEE land surface model to quantify impacts, trade-offs, and synergies of sustainable, Climate Smart Forest management scenarios for forest soils on Europe’s GHG balance, soil quality, and water budget under future climate conditions and disturbance regimes.
  • ORCHIDEE Milestone 4.1 [Luyssaert, Naudts, Marie, Jeong, Peylin, Vuichard, Yue, Ghattas, Valade, Maignan, McGrath, Guenet, Ottle, Flores, Wang, Bastrikov]
    Developing and maintaining the ORCHIDEE land surface model.
  • CLIMPRO [Luyssaert, Marie, Jeong, Jactel]
    Enhance the capability of ORCHIDEE to simulate abrupt mortality from storms, fires, drought, and pests and their biogeochemical and biophysical interactions.
  • ABC [Cornelissen, Bokhorst, Huisman, Ciric, Convey, Veraverbeke, Ellers, van Logtestijn, Fleming, British Antarctic Survey]
    The Antarctic biota count: a functional trait-based approach to scale biodiversity and its ecosystem impact from plot to region. NWO-funded.
  • How animal-mediated mutualistic microbiomes modulate the environmental sensitivity of savanna carbon dynamics [Cornelissen, de Jong, Veldhuis, Berg, Olff, van Logtestijn, Weedon, Kiers]. NWO-funded.
  • Loglife [Cornelissen, van Logtestijn, Berg, Tuo, Fujii, Chang, Loglife Team with Wageningen University and Utrecht University]
    Tree cemetery experiment to study the role of deadwood traits of different tree species in forest carbon turnover and biodiversity.
  • FLARE [Cornelissen, Zhang, van Logtestijn, Aerts, van der Werf]
    Fire Laboratory Amsterdam for Research in Ecology – with a focus on plant species effects on litter and vegetation flammability.
  • The effects of alien species on ecosystem functioning in polar habitats [Aerts, Bokhorst, van Loon-van Egmond, Convey, Cornelissen, British Antarctic Survey]
  • The impact of multiple extreme events on polar ecosystems [Aerts, Bokhorst, Heinzelmann]
  • Effects of salinization on Dutch peatland ecosystems [Aerts, Witte, Huizinga, Franken]
  • RETRAIT [Berg, Cornelissen, Ellers, Dias]
    Understanding the impact of environmental change on ecosystem processes using Response-to-Effect trait frameworks.
  • VeenVitaal [Berg, Ellers, Halfwerk, Aerts, Cornelissen, Weedon, IVM and Athena]
    Towards a sustainable and dynamic peat landscape for farmer, nature manager, citizen and biodiversity.
  • BIOBUILD [Berg, Cornelissen, RUG]
    Understanding the role of ecosystem engineers in community assembly, ecological networks and ecosystem stability using trait-based approaches.

2 – Plant-soil-microbe interactions

Plant roots and the soils they live in host one of the most diverse microbial communities on our planet. The free living and symbiotic microbes that make up these communities  have  profound effects on plant health and productivity, ecosystem processes, and contribute to the regulation of globally-important biogeochemical cycles. In this research theme we use a combination of advanced molecular techniques, high-throughput imaging, state of the art microscopy and biochemical approaches to examine: rhizosphere community ecology, the evolution of symbioses and soil biogeochemistry from a microbe-centric view.


  • MiCrop [Weedon, Kokkoris, Kiers, Stewart, Klein, van Son]
    We study the evolution of plant-microbiome interactions and identify opportunities for future plant breeding at an unprecedented scale. Our focus is on understanding stress-adaptive microbiomes and their active recruitment by plants across the plant kingdom through a phylogenetic approach. NWO-funded in collaboration with UvA, UU, NIOO-KNAW, WUR.
  • Tracking trade across symbiotic networks [Shimizu, Kiers, Oyarte Gálvez, van Son, Bisot, Cargill]
    In collaboration with AMOLF, we are developing an imaging robot to capture time-lapse imaging of network topologies. We use transformed in-vitro root systems with precisely controlled nutrient landscapes to generate high-resolution datasets for fungal architecture.
  • Flows, Structure and Trading in Underground Fungal Networks [Kiers, Oyarte Gálvez, Kokkoris, van Son, Terry, Bisot]
    The project’s goal is to understand how symbiotic fungi process and share complex information across their bodies to execute trading strategies with their host plants. This includes testing how mycorrhizal networks modulate electrical activity (voltage changes across cell membranes) in response to nutrient stimuli. NWO-funded.
  • SPUN [Kiers, Kokkoris, Klein, Stewart, Pringle]
    In collaboration with researchers, campaigners and local communities, the Society for the Protection of Underground Networks (SPUN) aims to accelerate efforts to protect underground ecosystems largely absent from biodiversity and climate agendas. We are building an open source mapping platform of Earth’s underground fungal biodiversity, developing a methodology for measuring and monitoring network identity and functioning, and translating the science into insights that are accessible to the world. 
  • A-LIFE Early Career support program [Kokkoris, Tutucci, van Otterdijk, van Son]
    This projects lands in the intersection between microbiology, fluorescence microscopy and technology development. Here, via the development of novel imaging and microscopy techniques (DNA/RNA FISH & Immunofluorescence) we examine the mysterious multinucleate biology of the most widespread plant related symbiotic fungi.
  • NUCLEAR MIX [Kokkoris, Kiers, van Otterdijk, van Son]
    By using high resolution molecular techniques, advanced microscopy, image analysis, and DNA/RNA fluorescence in situ hybridization, here, we examine how mycorrhizal fungi connect and exchange nuclei and what is the cost and benefit of these nuclear mixing.

3 – Species interactions and evolutionary adaptation

Evolution had led to an astonishing biodiversity. In this research line we study how natural and sexual selection drives trait evolution and adaptation of species to their abiotic environment and through symbiotic interactions with other species. We use field studies on natural populations, as well as laboratory evolution and omics studies to understand the adaptive consequences of variation at the genetic and phenotypic level.  Of particular interest are the ecological and evolutionary effects of  anthropogenic changes, such as urbanization and climate change. Our study systems cover a wide range of organisms including frogs, snails, insects, soil fauna, and fungi.


  • Citisex [Halfwerk, Cronin, Moran, Smit, Jerem]
    Understanding the role of sensory ecology and species interactions during sexual signal adaptation to an urbanizing world.
  • Camosense [Halfwerk, Berg]
    Unravelling how predators drive camouflage in the visual and acoustic sensory domain of their prey to avoid detection and predation.
  • Seminal fluid proteins (SFPs) in simultaneously hermaphroditic snails [Koene, Nakadera, Chen]
    Revealing the full identity, functions, and evolution of SFPs in freshwater snails.
  • Bizarre reproductive behaviours: physiology, morphology and evolution of love darts and other sexual attributes in hermaphroditic animals
    Testing how accessory-gland-product-injecting mating devices work and evolve, and whether predictions from sexual selection theory apply.
  • Happy snails [Nakadera, Koene, Ilyaskina, Leonards, Lamoree]
    Quantifying how invertebrates are impacted by pharmaceutical pollutants, such as antidepressants.
  • Anthropogenic impacts on snails [Koene, Nakadera, Zizzari]
    Investigating the impacts of temperature change and artificial lights on snails’ performance.
  • Ginger snail project [Nakadera, Koene]
    A newly discovered shell colour variant – why are they there? How do they make their shell red?
  • ARE-Robot evolution [Ellers, Eiben]

    Applying evolutionary computation techniques to evolve the overall design for real and simulated autonomous robots.

  • HiddenBiodiversity [Berg, Ellers]
    Improving urban green infrastructure by incorporating hidden biodiversity networks.

4 – Stress ecology and ecogenomics

Environmental and chemical stressors are omnipresent, demanding evolutionary adaptations to optimize organismal fitness and prevent population decline. In this research theme we investigate mechanisms of (chemical) stress response and of adaptation to different environmental conditions at different levels of biological organization, and at different time scales. In ecotoxicology, we study the effect and bioaccumulation of chemical stressors in soil invertebrates, also in relation to environmental conditions like soil properties and bioavailability. With a wide range of (eco)genomics and functional genetic approaches we study the evolutionary history of populations and aim to identify mechanisms of evolutionary adaptation. Finally, we apply genomics to understand inbreeding in endangered populations and facilitate conservation using genome sequence information.


  • DrComics [van Gestel, Hoedjes, Ellers, Bakker][LP1]
    Dose-response Curves for –OMICS data in soil quality assessment, especially in assessing the effects of pesticides to soil invertebrates.
  • PRORISK [van Gestel, Berg, Fernandes]
    Exploring the role of soil organisms in relation to ecosystem services and its potential sensitivity to chemical stressors.
  • Scaling for bioavailability [van Gestel, van Hall]
    Assessing the effect of soil properties on the toxicity of pesticides to soil organisms.
  • PAPILLONS [van Gestel, Berg, van Loon]
    Determining the interaction between micro- and nanoplastics and soil organisms. 
  • PFAS [van Gestel, Xie]
    Exposure, hazard and risk of PFAS in aquatic and terrestrial ecosystems.
  • Single nucleotide variants in life history evolution [Hoedjes]
    Identifying natural alleles responsible for ageing and fecundity evolution in the fruit fly.
  • What makes inbreeding so depressing? [Bosse]
    A genomic perspective on the role of harmful mutations in inbreeding depression.
  • Asian Elephant Genomics for Conservation [Bosse, Kappelhof]
    Genomic analysis of captive and wild Asian elephant populations to understand population structure and inbreeding.
  • Functional genomics of Drosophila life-history evolution [Beets, Hoedjes, Bosse]
    From high impact mutations to developmental adaptation in Drosophila: a novel framework to Integrate functional prediction from genome sequence with experimental validation using CRISPR-cas.
  • Omics of feral swine ASF susceptibility [Barmentlo, Bosse]
    Genomics and transcriptomics approach to predict feral swine response to African Swine Fever.