Fungal Ecology Lab (Rasmus Kjøller)

In the Fungal Ecology Lab, we are interested in how fungi are distributed in ecosystems, how fungi interact with plants and with each other and how fungi contribute to ecosystem functions.

We apply molecular markers to disentangle the otherwise invisible fungal populations and communities associated with plants and soil. We map fungal communities in time and space, how environment filters affect fungal communities and how changes in fungal community composition feedback on ecosystem functions.

As model organisms, we work with symbiotic root colonizing mycorrhizal fungi as well as phyllosphere associated fungal communities including plant pathogens.

Besides the use of molecular markers, we are competent at applying biochemical markers as well as classical microscopic examinations to fungi.

Another methodological strongpoint are various mesh-enclosure techniques to study both the function and community of in particular mycorrhizal fungal mycelia in soil.




Soil provides multiple ecosystem services to humans of course as being the fundamental basis for agricultural food production but also by storing carbon and providing clean drinking water. Soil aggregation correlates with SOM content, aeration and soil biodiversity. A healthy and fertile soil is well aggregated. Soil aggregation is a process where soil minerals and organic matter is enmeshed into a biological web including fungal hyphae and a matrix exuded by microbes. In Aggregate we wish to determine which soil biota are most important for the soil aggregation process across a range of different Danish soils with focus on fungal activity and hyphae. We also want to pinpoint potential troubles for the aggregation process - in specific of pesticides. The harmful side-effects of pesticides on soil health is further explored in the project GENEPEASE II. The two together will provide recommendations towards managing our agricultural soil resources in a sustainable way.

Fungi are, primarily, plant dependent organisms – either as saprotrophs that gain energy and nutrients by decomposing dead plant material or as biotrophic symbionts that obtain their carbon (C) directly from interactions with living plants. The most abundant group of fungal biotrophs are mycorrhizal fungi and, even though they obtain C – and thereby energy – from living plant cells, they also explore the soil for other nutrients, particularly nitrogen which they trade for C with their host trees. We, therefore, predict that litter quality has a significant impact on mycorrhizal fungal communities, and that their (response) traits should reflect the challenges associated with the litter input as a C source. We will investigate this by measuring mycorrhizal fungal traits across plots with four different tree species varying in litter quality, replicated in a unique common garden experiment found at six sites across Denmark.

Ensuring sustainable food production for a still growing world population while at the same time minimize the use of pesticides in agricultural production systems is an intriguing challenge. In the Matrix project (Microbiome Assisted Triticum Resilience in X-dimension) we explore the potential of the indigenous wheat microbiome which focus on the phyllosphere to provide health and sustainable growth of wheat. We test the microbial interactions among the microbiome constituents, the microbiome-plant interactions as well as the potential of the microbiome to combat common fungal diseases and mitigate drought stress. We also map the genomic and metabolic diversity among our isolated strains and all data are modelled in deep learning neural networks. The end goal is to provide either management regimes or apply specifically designed and safe SynComs for improved plant health. The project is a large collaborative project with multiple partners from UCPH, DTU, NIOO (Netherlands) and North Caroline State University.

A long-term focus within our research portfolio is community-, molecular- and functional ecology of mycorrhizal fungi. Themes investigated are:
1) The development of ectomycorrhizal fungal abundance and community composition with forest age, between hosts
3) The influence of forestry management practices on ectomycorrhizal fungal abundance, community composition and functioning
2) Common mycelial network between arbuscular mycorrhizal species
4) Primary succession of fungal communities with emphasis on arbuscular mycorrhizal fungi





Current funding includes four projects: Biological aggregate formation towards a healthy soil – AGGREGATE (NNF to 2025),  Microbiome Assisted Triticum Resilience In X-dimensions – MATRIX (NNF, to 2025), Pesticide Effects on Agricultural Soil Ecosystems – GENPEASEII (MST, to 2026) and Above and belowground interactions in forests (DFF, to 2026).





Contact Rasmus if you are interested in BSc or MSc projects on any aspect of fungal ecology. If you have a general idea of the topic, we can develop this into an exciting project together.

 Current student’s projects includes:

  • Plant protection potential of fungal foliar endophytes on wheat
  • Common mycelial networks between co-cultured Lupines and other crops
  • Involvement of arbuscular mycorrhizal fungi in soil aggregation
  • Bd (chytridiomycosis) prevalence in different Microhabitats in the Monteverde, Costa Rica

We also have a list of specific project suggestions. Check these out on - search for Rasmus Kjøller.




Name Title Phone E-mail
David Alejandro Castro Moraga Postdoc +4535327064 E-mail
Jesper Liengaard Johansen Assistant Professor +4535332317 E-mail
Rasmus Kjøller Associate Professor +4535322311 E-mail
Tobias Norman Master Student, Batrachochytrium dendrobatidis (Bd) in Costa Rica   E-mail
Elise Ida Blum Samuelsen Master student, Common mycelial networks in ECM, Supervised with Anders Michelsen   E-mail
Andrea Therese Kaaber Master students, Common mycelial networks in ECM, Supervised with Anders Michelsen   E-mail
Jon Mølgaard Michelsen Master Student. Community mineralization of organic fertilizer driving hydroponic protein crop growth. Supervised with Dorthe Horn Larsen (PLEN) & Flemming Ekelund   E-mail
Sanjana Sudheer Bhat Master Student. Seedling recruitment into Common Mycorrhizal Networks   E-mail
Ieva Marija Sokolovaite Master Student. Network complexity and C transfer between plants in a common mycorrhizal network. Supervised with Anders Michelsen   E-mail
Hongyi Wang Master Student. PHR-SPX network regulating AMF symbiosis in plants under light level changes   E-mail
Alma Njeri Agha Master Student. Botanical Rewilding: Can we rehabilitate degraded landscapes using soil and fungi inoculum? Supervised with Lars Båstrup-Spohr   E-mail


Alumni Type   Link 
Marta Gil Martínes Postdoc Link
Qian Lyu PhD Link
Thomas Rumle Thaaning Jensen MSc Link
Robin Mikaela Kotsia MSc Link
Jonas Thomsen MSc Link 
Jens Rasmus Plantener Jespersen MSc


Toke Bang-Andreasen PhD Link 
Carla Cruz Paredes PhD Link
Klara Rask MSc Link
Tue Rønhave MSc Link
Nanna Slaikkjer Pedersen MSc


Karina Cavour Jagd Frederiksen MSc  
Marie Merrild PhD Link
Christoffer Bugge Harder MSc Link
Tobias Gulberg Frøslev PhD Link
Kirsten Føns MSc Link


Fungal Ecology Lab

Associate Professor Rasmus Kjøller
Terrestrial Ecology Section
Universitetsparken 15
DK-2100 Copenhagen Ø, Denmark

Phone:  +45 35322311