Ecosystem Mycology

We study the role of fungi in ecosystems. We look at fungal communities in different environments as well as how changes in fungal communities feeds back on ecosystem processes. We aslo look at populations of important fungal plant pathogens and how they interact with their hosts. Most studies involve DNA sequencing for recognizing fungal species or genotypes from environmental samples. For an overview of current research projects visit my official UCPH homepage: Rasmus Kjøller

Current lab members

Associate Professor Rasmus Kjøller Fungal Community Ecology, Ecosystem Mycology
PhD student Toke Bang-Andreasen (supervised with Carsten Suhr Jakobsen, AU) Wood ash effects on soil bacteria
PhD student Ricoardo Pires (exchange from Sao Paulo, Brazil) Wood inhabiting  fungi
MS student Jens Rasmus Plantener Jespersen (supervised with Alvaro Lopez Garcia and Søren Rosendahl) Mycorrhizal status in primary succession plant communities
BS student Rasmus van Deurs

Oister mushroom production

Guests in the lab

Alvaro Lopez Garcia Post doc with Søren Rosendahl (Ecology and Evolution) in a collaborative project on AMF community assembly in primary succession series
Susana Santos Post doc in collaboration with Hans Henrik Bruun. Linking  molecular diversity in above-ground ground plant parts with soil, roots and litter


Tobias Gulberg Frøslev Finished he's BIOWIDE project at the end at 2017 and is currently working the project SoilTracker (UCPH-SNM)
Klara Rask Finished her masters thesis on heavy metals, plants and mycorrhiza in fall 2017 (with Fleming Ekelund)
Karina Cacour Finished her masters thesis on Rhizoscyphus ericae early in 2018
Sissel Fredsgaard Finished her masters thesis on orchid mycorrhizas and trophic status of Danish orchids in summer 2017 (with Flemming Ekelund)
Melanie Montes Finished her PhD on Population genetics of Phytophthora infestans in spring 2017 (with Søren Rosendahl)
Carla Cruz Paredes Finished her PhD "Wood ash effects on soil fungi" in April 2017 and is now working as a post doc with Iver Jacobsen (UCPH, PLEN)
Nanna Slaikjer Petersen Finished her masters thesis "Alternaria on Danish potatoes, populations and biology" in February 2017

Examples of current or suggested master or bachelor thesis projects:

Lauritz W Olsons legat giver speciale studerende i Mykologi ved KU mulighed for støtte i forbindelse med deltagelse i kongresser og kortere forskningsophold i udlandet mm.

Rasmus Kjøller, tlf.: +45 51 82 70 27, E-mail:
Universitetsparken 15, byg. 1, 2. sal (Terrestrisk Økologi)

Ectomycorrhizal fungi – biodiversity, community structure and function
Ectomycorrhiza is the symbiosis between many trees and basidiomycetes and ascomycetes fungi. The symbiosis is the dominating mycorrhizal symbiosis across the tree belt i.e. in temperate and boreal areas across northern US/Canada, northern Europe and Siberia. As each root tip is colonized by one fungus the composition of ectomycorrhizal communities can be assessed relatively easily in comparison with many other microbial communities. Basically, I am interested in all aspects of ectomycorrhizal communities, e.g. assembly rules, habitat filtering, competition, host specificity, response to anthropogenic compounds or environmental changes, fungal traits and especially the feed backs between fungal community structure and ecosystem processes.

Improving growth of cacao and coffee seedlings by inoculating with beneficial bacteria and fungi
When cacao and coffee plantations are established, seedlings are initially grown for 4 month in the nursery before being planted out. Seedlings are grown in an artificial growth substrate. This allows for growth promoting bacteria or fungi to be added without competition from indigenous populations until out-planting. Any increase in growth or health of seedlings will be economically beneficial for the local cacao and coffee producers. Both practical and theoretical literature based projects are possible. The project may, depending on interests, involve work at the center for tropical agroforestry, CATIE, in Costa Rica*

Analyzing a large meta-barcoding dataset of fungi responding to global change
Samples were taken in Abisko North Sweden in an experimental field manipulation simulating future climate change. Replicated treatments included heating, shading and fertilization. Fungal meta-barcoding sequence data was generated using the 454 platform. Sequences quality and depth per sample are excellent and some rudimentary data analysis has been done. The projects will allow you to become familiar with bioinformatic pipelines for meta-barcoding data, multivariate statistics of sample/species matrixes and writing and publishing original research.  

Populations, incidence and disease and virulence of foliar pathogens in Danish agriculture  
Agriculture is constantly threatened by diseases thriving in our human made monocultures. Foliar plant pathogenic fungi are among the worst combatants as these evolve fast due to short generation times and have large dispersal potential. Constantly agricultural practices need to be up to date with changing populations known diseases or to entirely newly arrived species. Projects within this area may target disease incidence, virulence of strains, population structure, and resistance to fungicides or other control measures.

Ectomycorrhiza and soil formation – Salix (Willow) as a main driver in primary succession series
Peberholm was established 1995-1998 by pumping up calcareous clay, sand and gravel from the bottom of Øresund. The island therefore provides a perfect opportunity to study primary succession. Today, most of the island is covered by low vegetation of herbs and grasses in symbiosis with arbuscular mycorrhizal fungi in a soil containing very little soil organic matter content. Patches of Salix in symbiosis with ectomycorrhizal fungi (EMF) are beginning to appear. Within these, changes are apparent: a more protective environment is present and soil formation speeds up which provide opportunities for new organisms to invade. Depending on interests, a project could study: the influence of Salix patch size/age on EMF community composition and formation of soil organic matter (SOM), quantify the contribution of EMF external mycelia into SOM and the inoculum potential (spore bank) of EMF in patches versus non-EMF soil as well as in the air.

Exploring the transcriptome of ericoid mycorrhizal fungi
Rhizoschyphus ericae is the dominating mycorrhizal symbiont of ericaceous plants in heathland systems around the world. From classical growth experiments the fungi is renowned for its great decomposing potential. The dogma is therefore that this fungus allows peatland soils to be explored especially for recalcitrant nitrogen which is then exchanged for sugar at the plant-fungal interface. This project will explore this symbiosis in the omics era e.g. using transcriptomic or meta-transcriptomic profiling of the fungus in contact with different types of substrates. Internship at the James Hutton Institute in Aberdeen and /or at Lund University is to be expected*

Mutualist and cheaters in plant-mycorrhizal interactions
Many argue that plants have evolved mechanisms to support good symbionts with more photosynthetically derived C than less good symbionts. Good symbionts are symbionts providing better services for the plant e.g. nutrient uptake from the soil in the case of mycorrhizal fungi. Given the general acceptance of this idea, actual observations from nature are scarce! This relies on the extreme difficulty in tracking plant C to specific symbiont species or genotypes and vice versa for nutrients taken up. Ectomycorrhizal symbiosis may provide an unexplored opportunity, as single root tips of trees are colonized by distinct fungal genotypes. Thereby C (14C labeled) from the plant can be traced to these individual tips and so can reciprocal uptake of e.g. 15N labeled N-compounds.

What regulates tree-line expansion in the Arctic due to climate change?
Due to climatic changes it is expected that the tree line in sub-arctic and mountainous regions will move north and up. The changes in vegetation from heathland to forest will most likely result in a change in C stored potentially adding further to the greenhouse effect. In order for tree seedlings to establish above the tree-line there must be both suitable microsites for germination. To study factors regulating tree seedling establishment, seedlings of Betula pubescens and Pinus sylvestris were transplanted into plots dominated by one of three moss species and into plots where mosses had been removed. During summer, temperature was increased in half of the plots by using OTC’s. In 2014 seedlings were harvested and mycorrhizal colonization and root length was measured. Furthermore, samples for determination of the ectomycorrhizal fungal community structure were taken and are ready for sequencing. The projects will allow you to become familiar with PCR and sequencing, multivariate statistics of sample/species matrixes and writing and publishing original research. The project is in collaboration with PhD student Signe Lett at Umeå University.