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Magnus Karlsson

Magnus Karlsson
I am interested in microorganisms and their interactions, with plants, with other microbes and with the environment. My current focus includes fungal interactions in relation to plant pathology and biological disease control.


Various microorganisms are constant threats to crop production on a global scale. Bacteria, fungi, oomycetes, viruses and nematodes cause yield losses and quality reduction before harvest, as well as during storage. Understanding the mechanisms of disease development is important when deciding strategies for efficient disease control in agriculture. Fungal infections on plants can be controlled by multiple approaches within an integrated pest management context. Biological control of diseases and disease-resistant crops can contribute to sustainable plant protection strategies. The current focus of my research is to understand mechanisms that parasitic fungi use to interact with plant hosts and other microbes, and how this results in diseased or healthy plants. I also study the resistance biology of plants, i.e. what plant factors that contribute to the ability to resist pathogen attack.

More information


Population genomics of the mycoparasite Clonostachys rosea

Biological control of plant diseases in agricultural production is an attractive alternative to the extensive use of chemical pesticides, and is therefore expected to be used in organic production and integrated pest management (IPM). However, biocontrol traits are complex and considered to be highly strain-specific. The objective of the proposed project is to investigate the genetic basis of biocontrol efficiency in the fungal biological control agent (BCA) Clonostachys rosea, and to identify high performing individuals for biocontrol of fusariose (caused by Fusarium spp.) on wheat. We will re-sequence the genomes of 70 C. rosea individuals, and evaluate these individuals with regards to; a) control of fusariose on wheat, and b) compatibility with the Proline fungicide used for chemical control of fusariose. A limited number of high- and low-performing individuals will be further evaluated in short field experiments, in order to confirm the results from the laboratory-based experiments. We will then correlate genotypic (gene and allele content) and phenotypic variation, and identify genes and gene families that distinguish high-performing individuals. This study will result in a better mechanistic understanding of biological control, and identify high-performing BCA individuals for control of fusariose on wheat in IPM.

Biological control of nematode diseases

Biological control of fungal diseases

Certain fungi lives as parasites on other fungi, and can be referred to as hyperparasites. We can use these hyperparasites to control plant pathogenic fungi causing diseases on our crop plants. Examples on hyperparasites used commercially today are different species from the fungal genera Trichoderma and Clonostachys. Several products are available on the market and research is done with the aim to develop more products and to make full use of their potential. A key factor for succeeding with our ambition to improve and optimize the use of hyperparasites is a deeper understanding of the mechanisms that results in efficient biological control. We study mechanisms employed by Trichoderma and Clonostachys species to interact with and antagonize plant pathogenic fungi and to improve plant growth. For this purpose, we use a variety of techniques, from field trials to genetic and molecular approaches.

Results from this work shows that the ability to control plant pathogenic fungi varies considerably between individuals of the same hyperparasite species. This means that it matters which individuals that are used for biological control of different plant diseases. New techniques for large-scale analyses of complete genomes of fungi have revolutionized our understanding of the genetics behind complex traits such as biological control. This work have the potential to result in genetic markers that can facilitate identification and selection of highly efficient individuals for biocontrol, for formulation and storage, and for combinations with other biological, chemical or physical control measures. In the long-term, breeding programs for biological control organisms are plausible.

The extensive use of chemical fungicides can result in development of fungicide resistance in fungal plant pathogen populations. Our ongoing research investigates the possibility to alternate between chemical and biological control measures during the growing season, in order to prevent development of fungicide resistance. This is currently investigated for septoria tritici blotch in wheat and grey mould on strawberry.

Breeding for root rot resistance in pea

The objective of this project is to develop new pea varieties with resistance towards root rot disease, in combination with excellent production properties. The disease is mainly caused by the oomycete Aphanomyces euteiches. Currently, neither pea varieties with resistance nor chemical pesticides are available for growers. However, a non-commercial pea variety (PI180693) is partially resistant to aphanomyces root rot, and can be used for studies of resistance trait and be the starting point for commercial breeding. We will utilize high-throughput genotyping to identify genetic markers that co-segregate with root rot resistance. These markers will then be used to speed up the plant breeding program by improving precision in the selection of resistant plants for further evaluation. Studies of the population structure and virulence of the pathogen will enable optimal choices of pea cultivars in different countries and regions. Having pea varieties with resistance towards aphanomyces root rot promises to be a very efficient plant protection strategy, which is compatible with principles of integrated pest management and organic farming.

Small-RNA based strategies to control fungal plant pathogens

In this project, the main focus is on a new biocontrol method based on small RNA (sRNAs) and the biological process called RNA interference (RNAi). Small RNAs play variety of roles in organisms and are key factors in interactions between hosts and their parasites, pathogens and symbionts. During interactions, sRNAs travel from one species to another and modulate regulatory machinery of host cells through targeted gene silencing. Present proposal aims to i) characterise the RNAi machinery and its biological functions in biocontrol fungus Clonostachys rosea, ii) identify if, or to what extent, sRNAs are key determinant of biocontrol interactions in C. rosea and if so their potential target genes in interacting organisms and iii) evaluate the potential application of sRNAs in controlling fungal plant diseases. We will use 1) Fusarium graminearum- wheat and 2) Botrytis cinerea- strawberry as model pathosystems to evaluate the prospect of exogenous applications of sRNAs for crop protection. Selection of pathosystems is based on the fact that Fusarium head blight and foot and root rot pose serious threats world-wide for food safety including mycotoxin contamination in cereals and maize, while B. cinerea causes a serious risk to several vegetables, fruits and flowers in their pre- and post-harvest stages by causing grey mould disease. Our findings will expand the understanding of how sRNA-based biocontrol mechanism can be exploited for future plant disease control.

Read more about biological control using fungi here

Read more about resistance breeding in plants here (in Swedish)








Professor at the Department of Forest Mycology and Plant Pathology; Division of Plant Pathology
Telephone: +4618-671837
Postal address:
Skoglig mykologi och växtpatologi , Box 7026
750 07 UPPSALA
Visiting address: Almas Allé 5, Uppsala