Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences
Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

Institutionen för skoglig mykologi och växtpatologi

Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

Dan Funck Jensen

Professor, Plant Pathology


Dan Funck Jensen (2001-2015):

Papers with peer review and book chapters

Karlsson M, Brandström-Durling M, Choi J, Kosawang C, Lackner G, Tzelepis G, Nygren K, Dubey M, Kamou N, Levasseur A, Zapparata A, Wang J, Amby D, Jensen B, Sarrocco S, Panteris E, Lagopodi A, Pöggeler S, Vannacci G, Collinge D, Hoffmeister D, Henrissat B, Lee Y, Funck Jensen D (2015) Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea. Genome Biology and Evolution 7:465-480.
Hosseini S, Resjö S, Liu Y, Brandström-Durling M, Heyman F, Levander F, Liu Y, Elfstrand M, Funck Jensen D, Andreasson E, Karlsson M (2015) Comparative proteomic analysis of hyphae and germinating cysts of Phytophthora pisi and Phytophthora sojae. Journal of Proteomics 117:24-40.

Tzelepis G., Hosomi, A., Hossain T.J., Hiroto Hirayama, H., Dubey, M., Jensen, D., Suzuki, T., Karlsson, M. (2014). Endo-b-N-acetylglucosamidases (ENGases) in the fungus Trichoderma atroviride: Possible involvement of the filamentous fungi-specific cytosolic ENGase in the ERAD process. Biochemical and Biophysical Research Communications 449: 256-261.

Dubey MK, Jensen DF, and Karlsson M (2014). An ATP-binding cassette pleiotropic drug transporter protein is required for xenobiotic tolerance and antagonism in the fungal biocontrol agent Clonostachys rosea. Molecular Plant-Microbe Interaction, Molecular Plant-Microbe Interactions 27 (7): 725-732.

Tzelepis G, Melin P, Stenlid J, Funck Jensen D, Karlsson M. 2014. Functional analysis of the C-II subgroup killer toxin-like chitinases in the filamentous ascomycete Aspergillus nidulans. Fungal Genetics and Biology, Fungal Genetics and Biology 64: 58–66

Kosawang C, Karlsson M, Vélëz H, Rasmussen PH, Collinge DB, Jensen B and Jensen DF 2014. Zearalenone detoxification by zearalenone hydrolase is important for the antagonistic ability of Clonostachys rosea against mycotoxigenic Fusarium graminearum. Fungal Biology

Dubey, MK,  Funck Jensen D and Magnus Karlsson. 2014. Hydrophobins are required for conidial hydrophobicity and plant root colonization in the fungal biocontrol agent Clonostachys rosea. BMC Microbiology, 14:18.

Kosawang, C, Karlsson, M, Funck Jensen, D, Dilokpimol A, and Collinge, DB. 2014. Transcriptomic profiling to identify genes involved in Fusarium mycotoxin Deoxynivalenol and Zearalenone tolerance in the mycoparasitic fungus Clonostachys rosea. BMC Genomics, 15:55.

Hosseini S, Heyman F, Olsson U, Broberg A, Funck Jensen D, Karlsson M. 2013. Zoospore chemotaxis of closely related legume-root infecting Phytophthora species towards host isoflavones. Plant Pathology doi: 10.1111/ppa.12137

Dubey M, Broberg A, Funck Jensen D, Karlsson M. 2013. Role of the methylcitrate cycle in growth, antagonism and induction of systemic defence responses in the fungal biocontrol agent Trichoderma atroviride. Microbiology 159:2492-2500.

Dubey M, Broberg A, Sooriyaarachchi S, Ubhayasekera W, Funck Jensen D, Karlsson M. 2013. The glyoxylate cycle is involved in pleotropic phenotypes, antagonism and induction of plant defence responses in the fungal biocontrol agent Trichoderma atroviride. Fungal Genetics and Biology 58-59:33-41.

Jensen B., Knudsen, IMB., Andersen, B., Nielsen, KF., Thrane, U., Jensen, DF. and Larsen J., 2013. Characterization of microbial communities and fungal metabolites on field grown strawberries from organic and conventional production. International Journal of Food Microbiology 160: 313-322

Dubey MK, Ubhayasekera, W., Sandgren, M, Jensen, DF, Magnus Karlsson, M. 2012. Disruption of the Eng18B ENGase Gene in the Fungal Biocontrol Agent Trichoderma atroviride Affects Growth, Conidiation and Antagonistic Ability. PlosOne Vol 7 (5): e36152. Download.

Tzelepis GD, Petter Melin, P.,Jensen DF., Stenlid, J., Karlsson, M. 2012. Functional analysis of glycoside hydrolase family 18 and 20 genes in Neurospora crassa. Fungal Genetics and Biology  49: 717-730.

Hosseini S, Karlsson M, Funck Jensen D, Heyman F. 2012. Quantification of Phytophthora pisi DNA and RNA transcripts during in planta infection of pea. European Journal of Plant Pathology 132:455-468.

Louarn S, Nawrocki A, Edelenbos M, Jensen DF, Jensen ON, Collinge DB, Jensen B. 2012. The influence of the fungal pathogen Mycocentrospora acerina on the proteome and polyacetylenes and 6-methoxymellein in organic and conventionally cultivated carrots (Daucus carota) during post harvest storage. Journal of Proteomics 75: 962–977.

Sundelin T, Jensen DF, Lübeck M. 2011. Identification of Expressed Genes During Infection of Chinese Cabbage (Brassica rapa subsp. pekinensis) by Plasmodiophora brassicae. The journal of Eukaryotic Microbiology. 58 (4): 310-314. Download.

Mamarabadi, M., Jensen, DF., and Lübeck M., 2009. An N-acetyl-β-d-glucosaminidase gene, cr-nag1, from the biocontrol agent Clonostachys rosea is up-regulated in antagonistic interactions with Fusarium culmorum.  Mycological Research 113 (1): 33-43

Mamarabadi, M., Jensen B., Jensen, DF., and Lübeck M. 2008. Real-timeRT-PCR expressionanalysis of chitinase and endoglucanase genes in the three-way interaction between the biocontrol strain Clonostachys rosea IK726,Botrytis cinerea and strawberry. FEMS Microbiol Lett, 285 (1): 101-110

Jensen, DF., Knudsen, I.M.B, Lubeck, M., Mamarabadi, M., Hockenhull,J., Jensen, B. 2007. Development of a biocontrol agent for plant disease control with special on the near commercial fungal antagonist Clonostachys rosea strain ‘IK726’. Australasian Plant Pathology 36 (2): 95-101

Albertsen, A., Ravnskov, S., Green, H., Jensen, DF. and Larsen, J. 2006. Interactions between the external mycelium of mycorrhizal fungus Glomus intraradices and other soil microorganisms as affected by organic matter. Soil Biology and Biochemistry 38: 1008-1014.

Eilenberg, J., Jensen, DF. and Philipsen, H. 2006. Education in biological control at the university level at KVL pp 65-71. In: An Ecological Approach to Biological Control. J. Eilenberg and HMT. Hokkanen eds. 322 p.

Ravenskov, S., Jensen, B., Knudsen, IMB.,Bødker, L., Jensen, DF., Karlinski, L., and Larsen, J. 2006. Soil inoculation with the biocontrol agent Clonostachys rosea results in mutual inhibition, plant growth promotion and alteration of soil microbial communities. Soil Biology & Biochemistry 38: 3453-3462

Sarrocco, S., Mikkelsen, L. Vergara, M., Jensen, DF., Lübeck, M. and Vannacci, G. 2006. Histopathological studies of sclerotia of phytopathogenic fungi parasitized by GFP transformed Trichoderma virens antagonistic strains. Mycological Research 110: 179-187

Schiller, M., Lübeck, M., Sundelin, T., Meléndez, L.F.C., Danielsen, S., Jensen, D.F. and Ordeñana K.M. 2006. Two subpopulations of Colletotrichum acutatum are responsible for antracnose in strawberry and leatherleaf fern in Costa Rica. European Journal of Plant Pathology 116: 107-118.

Sundelin, T.,Schiller, M., Lübeck, M. and Jensen, D.F. 2005. First report of antracnose fruit rot caused by Colletotrichum acutatum on strawberry in Denmark. Plant Disease  89: 432.

Jensen, B., Knudsen, IMB., Madsen,M. and Jensen, DF. 2004. Biopriming of infected carrot seed with an antagonist, Clonostachys rosea, selected for control of seedborne Alternaria spp. Phytopathology 94:551-560.

Yohalem, DS., Nielsen, K., Green, H. and Jensen DF. 2004. Biocontrol agents efficiently inhibit sporulation of Botrytis aclada on necrotic leaf tips but spread to adjacent living tissue is not prevented. FEMS Microbiology Ecology 1613

Jensen, D.F., & Schulz, A. 2003. Exploitation of GFP-technology with filamentous fungi. chapter 33.pp 441-451.In: Handbook of Fungal Biotechnology, 2edition, Dilip K. Arora, Poul D Bridge and Deepak Bhatnager (Eds.). Marcel Dekker Inc., New York.

Mikkelsen, L., Sarrocco, S., Lübeck, M., and Dan Funck Jensen 2003. Expression of the red fluorescent protein DsRed-Express in filamentous Ascomycete  fungi. FEMS Microbiology Letters 223 (1): 135-139.

Jensen, B., Knudsen, I.M.B, Jensen, D.F. 2002. Survival of conidia of Clonostachys rosea on stored barley seeds and their biocontrol efficacy against seed borne Bipolaris sorokiniana. Biocontrol Science and Technology 12:427-441.

Lübeck, M. and Jensen, D.F. 2002. Monitoring of biocontrol agents based on Trichoderma strains following their application to glasshouse crops by combining dilution plating with UP-PCR fingerprinting. Biocontrol Science and Technology 12: 371-380.

Nielsen, K., Yohalem, D.S. and Jensen, D.F. 2002. PCR detection and RFLP differentiation of Botrytis species associated with neck rot of onion. Plant Disease: 86:682-686.

Rasmussen, P.H., Knudsen, I.M.B., Elmholt, S. and Jensen D.F. 2002. Relationship between soil cellulolytic activity and suppression of seedling blight of barley in arable soils. Applied Soil Ecology 19: 91-96.

Green, H., N. Heiberg, Lejbølle, K. & Jensen D.F. 2001: The use of a GUS transformant of Trichoderma harziaum, strain T3a, to study metabolic activity in the spermosphere and rhizosphere related to biocontrol of Pythium damping-off and root rot. European J. Plant Pathol. 107: 349-359.

Lübeck, M., Knudsen, I.M.B., Jensen, B., Thrane, U., Janvier C. and Jensen, D.F. 2001. GUS and GFP transformation of the biocontrol strain Clonostachys rosea IK726 and the use of marker genes in ecological studies. Mycological Research 106: 815-826.

Nielsen, K., Justesen, A.F., Jensen, D.F. and Yohalem, D.S. 2001.  Universally primed polymerase chain reaction alleles and internal transcribed spacer restriction fragment length polymorphisms distinguish two subgroups in Botrytis aclada distinct from B.byssoidea. Phytopathology 91: 527-533.

Mikkelsen, L., Roulund, N., Lübeck, M. and Jensen, D.F. 2001. The perennial ryegrass endophyte Neotyphodium lolii genetically transformed with the green fluorescent protein (gfp) and visualization in the host plant. Mycological Research 105 (6): 644-650.

Proceedings and other reports

Kosawang C, Karlsson M, Jensen B, Vélëz H, Have Rasmussen P, Collinge DB, Funck Jensen D. 2013. Detoxification of the Fusarium mycotoxin zearalenone is an important trait of Clonostachys rosea in biocontrol of Fusarium foot rot of barley. IOBC/wprs Bulletin vol. 86:133-136, Biological control of fungal and bacterial plant pathogens.

Dubey M, Ubhayasekera W, Sandgren M, Funck Jensen D, Karlsson M. 2013. The Trichoderma atroviride Eng18B ENGase gene product is essential for in vitro antagonism against Botrytis cinerea. IOBC/wprs Bulletin vol. 86:137-141, Biological control of fungal and bacterial plant pathogens.


I have been at SLU since April 2008 following a decision made by the NL-faculty to strengthen research in plant pathology with focus on agricultural crops. Before that I served as an associate professor in plant pathology at University of Copenhagen, Faculty of Life Sciences. My research in Denmark was focussing on root pathology, seed borne pathogens and post harvest diseases - with the main effort on biological control. Pathogens belonging to the genera Pythium, Fusarium, Botrytis, Alternaria, Mycocentrospora and Colletotrichum were in focus. Biocontrol work included isolation, screening, selection, production, formulation and delivery of biocontrol agents (BCAs) as well as efficacy testing under field and greenhouse conditions. Research relevant for risk assessments and EU registration of BCAs was also addressed. More basic research concerned microbial ecology of BCAs including molecular interactions with their host fungal pathogen.

Since my start at SLU we have built up a new research team of 6 researchers + 4 PhD-students. In this we have gathered complementing methodological competences so we now have a platform for exploiting technologies with filamentous fungi such as: Fungal transformation & gene constructions, DNA reporter technology (GFP, DsRed etc.), advanced fluorescent microscopy, gene knock outs and complementation, arrays and quantitative PCR, fungal characterization and diagnostic molecular tools as well as methods in evolutionary genetics. We are also building up expertise in next generation sequencing (454 sequencing and Solexa/Illumina) for studying community structures and gene expression in fungal host interactions. Several genomes including Clonostacys rosea and Phytophthora spp. have recently been sequenced and annotated in the research group and analysis of several transcriptomes from biocontrol or plant pathogen interactions are under way. 

Building on these competences we have made a research strategy with three main areas in focus:

  • Biocontrol: Fungal-Fungal interactions in relation to biological control of plant diseases
  • Pathogenicity: Fungal/oomycete – Plant host interaction
  • Cropping system and soil management: Microbial community structures and function in relation to plant health

The biological control program has origin in important disease problems in agriculture including root/stem base diseases, seed borne pathogens, pathogens infecting leaf and flowers and post harvest diseases. The research is trying to elucidate the basic biology in biocontrol interactions between pathogens, the host plant and biocontrol organisms (BCAs). Special attention is given to Trichoderma- based BCAs and a fungal BCA (Clonostachys rosea ‘IK726’) which was isolated in my Danish group several years ago and which has proven efficient in controlling several plant diseases in agricultural- and horticultural crops. We are interested in how the BCAs are attacking the pathogens and also how they can protect themselves in interactions with the plant pathogens. Transcriptome sequencing of ‘IK726’ is used among other methods for studying these biocontrol interaction. A new project started January 2013 which is funded by the research council Formas and is entitled: “Consortia of biological control organisms formulated for improving plant health - a novel technology for sustainable crop”. In this we will look at the possibility to combine C. rosea with other BCAs and in this way obtain additive, synergistic or complementary effects in biocontrol of several diseases in a plant crop. Our understanding of how consortia can be compatible with existing technologies such as application with fungicides in full or reduced dosages will be another outcome of the project. Project partners also include researchers from the microbiology department at SLU and the company Lantmännen BioAgri (read more).

A new area of research for us is biological control of post harvest diseases where we in a Nordic project are looking at biocontrol of storage diseases in potato (read more).

More practical aspects of exploiting biological disease control of diseases in agricultural crops are now addressed in collaboration with the agro industry and end users. The projects in this biocontrol program are further described on our Biological control page.

The program on pathogenicity is our part of a large Danish research program which I am coordinating from SLU – entitled ”Secreted proteins in fungal parasitic interactions for feed, food and non-food industry”. Our role in the program is to reveal secreted proteins involved in the interaction between Phytophthora pisi and pea – a new pathogen attacking pea plants. Our special interest is the role of secreted effectors as pathogenicity factors in root rot on pea and related species. In collaboration with the Beijing Genomic Institute (BGI, America) P. pisi and P. niederhauserii have now been genome sequenced. Through our international research network we now will have access to several other Phytophthora spp. genome sequences for use in this ongoing project. In more  general terms we are interested in what determines host range and specificity of root infecting Phytophthora spp.

In the program on cropping systems and soil management one project is addressing the effects of tillage and the preceding crop on soil microbial communities and plant disease in winter wheat. In order to understand the microbiological background to the differences in crop development, field observations and measurements are combined with molecular methods and bioassays. Special focus is on effects on the ability of plants to survive the winter period, and the role of early infections of Gaeumannomyces graminis var. tritici. Another project concerns the importance of crop residues for the survival of plant pathogenic fungi seen in relation to the functional diversity of microorganisms colonising the material. We investigate the persistence of Fusarium graminearum and Oculimacula yallundae, on decaying straw under varying conditions, and how the inoculum density is related to the ability of the pathogens to cause disease. Within the program we have close research collaboration with INRA-Dijon, France. In a new EU project “Optimising Subsidiary Crop Applications in Rotations” (FP7-KBBE-2011-5) we will especially focus on F. graminearum and F. culmorum in cropping systems with subsidiary crops.

Teaching: I am involved in teaching plant pathology at all levels (BSc, MSc and PhD) and is responsible for the MSc. course “Plant Pathology” running in the autumn at SLU-Ultuna. Read more on our Teaching pages.



Dan Funck Jensen

Professor, Avdelningen för växtpatologi

Telefon:   018-672798


Skoglig mykologi och växtpatologi , Box 7026
750 07 UPPSALA

Almas Allé 5, Uppsala

Sidan uppdaterad: 2015-03-24.

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