Dan Funck Jensen
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.
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.