The research in this theme is related to a wide range of biotic interactions and includes studies on plant interactions with viruses, bacteria, fungi, oomycetes, nematodes, insects and mites.


Plants interact with a wide range of organisms, some of which are harmful (e.g. pathogens and herbivorous insects), while others are beneficial (e.g. growth-promoting rhizobacteria and predatory enemies of herbivores). The research in theme 2 is related to this wide range of biotic interactions and includes studies on plant interactions with viruses, bacteria, fungi, oomycetes, nematodes, insects and mites. On the plant side Arabidopsis thaliana is often used as a model because of the ample opportunities that this fully sequenced plant species with many available well-characterized mutants and transgenics offers. In addition, various Brassicaceae species, barley, tobacco, clover, and economically important crops, such as potato, tomato, and their wild relatives are used. The research in theme 2 is divided into the subthemes (a) pathogenicity factors, (b) resistance, and (c) multitrophic interactions. The research in these subthemes ranges from studies on gene function and expression, to the discovery of novel cellular mechanisms, and phenotype expression in relation to interaction with plant attackers and their antagonists.

While the majority of studies in theme 2 focus on the individual plant and cellular level, more and more studies investigate plants as members of complex communities. Interactions with a single attacker modify the phenotype of the plant and, consequently, affect interactions with other community members. Unravelling the mechanisms and ecological functions of plants interacting with multiple species increases the complexity that investigators face. This complexity is both a challenge and a necessity as it is a first step towards unravelling the ecological relevance in terms of costs and benefits of the defensive mechanisms in a multitrophic context. Hence, a challenge for the more mechanistically oriented research in theme 2 is to put laboratory findings to the test in an ecological perspective. In this respect, theme 2 will highly benefit from the interdisciplinary theme "ecology" of EPS4.

State-of-the-art technology is exploited to identify loci and genes that play important roles in the plant or the attacker during plant-pathogen and plant-herbivore interactions. Techniques such as comparative genomic hybridization, virus induced gene silencing, RNAi, high-field NMR spectroscopy, QTL mapping in RILs, and confocal laser spectroscopy are utilized and further developed. Moreover, genomics techniques such as transcript profiling with DNA microarrays, phospho-proteomics, metabolomics through NMR or GC-TOF-MS, and kinome profiling with PepChips are well-embedded in the theme 2 research programmes. With the availability of (whole) genome sequences of an increasing number of economically important plant pathogens, a large number of candidate effectors are about to be discovered. This will be highly instrumental in the discovery of novel R-genes and aid in resistance breeding.

The complexity of the defense signaling networks that rapidly become uncovered, combined with the complex data sets that are associated with genomics research, theme 2 reached the phase in which a systems biology approach will move the field beyond the reductionist approach towards the identification of emergent properties that otherwise will remain undiscovered. The efforts of EPS towards developing and promoting the field of systems biology in plant science will be highly instrumental in implementing this research area in theme 2. Therefore, the interdisciplinary theme "systems biology" will be valuable for the development of this research area in theme 2.

The research on interactions between plants and biotic agents is subdivided and coordinated in the three following subthemes:

Subtheme 2a - Pathogenicity Factors

Pathogens and pest organisms that parasitize crop plants are diverse, ranging from viruses, bac­teria, fungi, oomycetes to nematodes and insects. Due to this diversity they utilize different mechanisms to recognize, penetrate, colonize, parasitize and/or multiply on the expenses of the plant. Viruses have been shown to contain different genes, which are essential for uptake and transmission in vectors and for multiplication and dissemination within host plants. The small size of plant virus genomes permits a study at the molecular level of pathogenicity factors in the context of their function in the virus replication cycle. Special attention will be given to the 'cell-to-cell' move­ment proteins encoded by viruses, which are essentially involved in establishing syste­mic infection through the plant, by modifying plasmodesmata, and to virally encoded suppressors of gene silencing, a natural defence system in plants against viruses. In addition, RNA-dependent RNA-poly­merases are pathogenicity factors unique to these pathogens. Much progress has been made in identifying pathogenicity and virulence factors of eukaryotic pathogens. By using tools such as cDNA-AFLP analysis, gene silencing and targeted gene disruption or gene replacement many genes have been identified that compromise virulence of these pathogens. Various potential virulence factors of nematodes, including cell wall degrading enzymes have been isolated. These functions were already known in necrotrophic plant pathogenic fungi and bacteria. Also evidence is accumulating that bacterial and fungal avirulence genes have a primary role in virulence (i.e. suppressing basal defence). Thus many avirulence factors interact with virulence targets, which are guarded by resistance proteins. Direct interactions between avirulence factors and resistance proteins is the exception rather than the rule. Future research is aimed at further dissecting elicitor receptor complexes and identifying proteins involved. The availability of the genome sequences of important pathogens will be highly instrumental in this subtheme.

Contributors to subtheme 2a:

  • Dr. G. van den Ackerveken (Plant-Microbe Interactions, UU). Molecular basis of disease susceptibility in Arabidopsis.
  • Dr. J.A.L. van Kan (Phytopathology, WU): Molecular genetic analysis of Botrytis species.
  • Prof.dr. F. Govers (Phytopathology, WU): The biology and pathology of the oomycete late blight pathogen, Phytophthora infestans.
  • Prof.dr. J. Bakker, Dr. A. Goverse, Dr. J. Helder, Dr. G. Smant (Nematology, WU): Compatible plant-nematode interactions.
  • Dr. R.J.M. Kormelink, Prof.dr. J.Vlak (Virology, WU): Replication and assembly of Tospoviruses.
  • Dr. M. Rep, Prof.dr. B.J.C. Cornelissen (Plant Pathology, UvA): Identification and functional analysis of pathogenicity factors of Fusarium oxysporum.
  • Dr. J.W.M. van Lent (Virology, WU): Cytology of virus infection.
  • Dr. G.H.J. Kema, Dr. T.A.J. van der Lee , Dr. C. Waalwijk (Biointeractions, PRI, WUR): Mycosphaerella and Fusarium research.

Subtheme 2b - Resistance

Various ways of resistance breeding have generated durable crop protection. However, due to high selection pressures highly uniform crop plants become susceptible to new variants of pathogens. It is important to understand the molecular basis of this adaptation in order to breed for more durably resistant plants. Therefore pathogen avirulence genes and their complementary natural plant resistance genes or gene clusters are isolated and studied in detail. Evidence is accumulating that resistance genes occur in clusters comprising many homologues. In natural populations balancing selection occurs where most resistance genes remain in the population and new specificities are continuously generated by meiotic or mitotic recombinations. In agricultural settings heavy selection pressure is imposed on pathogens forcing the generation of new virulent isolates giving rise to the so-called 'boom and bust cycle'. Much effort is focussed on disease resistance and mechanisms involved.

Also signal transduction pathways initiated after activation of resistance genes by avirulent pathogens are being studied. They include locally and systemically induced defense response mechanisms and programmed cell death. In some cases receptor complexes involving well-characterised elicitors, cognate resistance proteins and possibly virulence targets are studied. In addition, resistance mechan­isms are studied that are not associated with the hypersensitive reponse (HR), such as pre­haustorial and non-host resistance and avoidance. These resistances generally inherit quantitatively and a genetic approach is followed to identify the quantitative trait loci (QTLs). For this purpose mapping populations and back-cross inbred lines have been developed, as well as extreme phenotypes in which relevant genes have been accumulated. Transcriptome and proteome analysis are performed for HR and non-HR based resistance. Molecular genetic analyses of these resistances give strong evidence that the genes, involved in these resistances, are different from those involved in HR. Detailed studies will give further insight into the function of these genes and clues as to why they lead to more durable resistance. Hence, exploring host plant resistance will lead to optimal exploitation of these natural defense mechanisms.

Research on defense signaling cascades provided novel insights into the role plant hormones in the regulation of resistance against microbial pathogens and insect herbivores. More and more linear defense-related signal transduction pathways are uncovered and it becomes clear that these pathways cross-communicate to finely tune the plant's defense response depending on the attacker it is encountering. In addition, novel plant-derived signals, such as phosphatidic acid and various airborne plant volatiles are identified and their roles in the regulation of plant defense are elucidated. Moreover, signals derived from beneficial and pathogenic micro-organisms that interfere with the plant's immune response have been characterized. Examples are cyclic lipopeptide surfactants that are produced by non-pathogenic Pseudomonas rhizobacteria, nematode effectors, virulence factors produced by Verticillium dahliae, and phytotoxic proteins produced by Botrytis cinerea.

Contributors to subtheme 2b:

  • Prof. dr. B.P.H.J. Thomma (Phytopathology, WU): Arabidopsis guides research on tomato diseases.
  • Prof.dr. P.J.G.M de Wit (Phytopathology, WU): Identification and functional analysis of the effector catalogue of Cladosporium fulvum and related Dothideomycetes.
  • Dr. F. Menke, Prof.dr. B. Scheres (Molecular Genetics, UU): Quantitative phospho-proteomics of defense signaling in Arabidopsis.
  • Dr. H.J.M. Linthorst (Plant Cell Physiology, LU): Induced plant defense.
  • Dr. M.H.A.J. Joosten (Phytopathology, WU): Resistance and (a)virulence in the interaction between Solanaceous plants and their pathogens.
  • Dr. T. Munnik, Dr. C. Testerink, Prof.dr. M.A. Haring (Plant Physiology, UvA): Role of phosphatidic acid in plant defence signalling.
  • Dr. F.L.W. Takken, Prof.dr. B.J.C. Cornelissen (Plant Pathology, UvA): Uncovering the molecular mechanisms of R protein function.
  • Dr. Y. Bai, Dr. A.W. van Heusden, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Resistance breeding.
  • Prof.dr. R.G.F. Visser, Prof.dr. E. Jacobsen (Plant Breeding, WUR): In search for durable resistance against the potato pathogen Phytophthora infestans.
  • Dr. B. Vosman, Dr. R.E. Niks, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Breeding for insect resistant plants.
  • Prof.dr. J. Bakker, Dr. A. Goverse, Dr. G. Smant (Nematology, WU): R gene mediated resistance in potato.
  • Dr. A. Schots (Nematology, WU): Oral immune regulation of inflammatory bowel diseases.

Subtheme 2c - Multitrophic Interactions

Plants colonized by rhizobacteria or stimulated to attract carnivorous insects reduce the incidence or severity of plant disease or damage by herbivores. Natural defence mechanisms activated by rhizobacteria or damage by herbivorous insects have many characteristics in common. Research in this subtheme is directed toward unravelling the cross-talk between signal-transduction pathways involved in pathogen-induced systemic acquired resistance (SAR), rhizobacterially-mediated induced systemic resistance (ISR) and insect-induced direct and indirect defenses, using the model plant Arabidopsis and other host plants where appropriate.

Plant roots provide beneficial soil organisms with a suitable environment. The use of biocontrol bacteria is an alternative for the use of synthetic pesticides. Several non-pathogenic root- colonizing bacteria are able to decrease pathogen survival, reduce build-up of pathogen populat­ions, or counteract infection of susceptible plants. The mechanisms involved comprise competit­ion for nutrients, pro­duction of various antibiotics, and induction of disease resistance in the plant. Practical applications of biocontrol bacteria are often hampered by (i) insufficient antifungal activity, (ii) poor root colonization, and (iii) limited knowledge of disease-suppressive mechanisms in the natural soil environment. As biocontrol bacteria are likely to play a crucial role in plant protection under natural conditions, antagonistic bacteria are isolated from plants grown under these conditions. New types of antibiotics will be identified and regulation of important antibiotics will be studied in detail in the natural environments of biocontrol bacteria.

Above ground, often volatile chemical signals play an important role in the interaction between plants and insects. Herbivorous insects but also airborne pathogens recognize suitable host plants on the basis of plant constituents. The production of many of the plant metabolites involved is induced by wounding, or herbivory. Signals from conspecific herbivores and signals from their enemies can play a role as well. It is becoming clear that signal transduction pathways in induced plant-insect and plant-pathogen interactions have many characteristics in common. Detailed analysis of cross-talk between different plant-attacker interactions will be studied and major research themes comprise chemical and functional analysis of the signals involv­ed. A major focus will also be the interaction between aboveground and belowground attackers and the consequences for the final outcome of the defense reaction of the plant. We hope to be able to unravel divergence and convergence of signal transduction pathways for the different plant-attacker interactions. Knowledge at the molecular level of induced plant responses allows the careful manipulation of the plant phenotype. This provides excellent tools for ecological investigations on the effects of particular plant traits in interactions with plant pathogens, herbivorous insects and their natural enemies. This will be an important route towards a novel ecogenomics approach.

Contributors to subtheme 2c:

  • Prof.dr. H.J. Bouwmeester (Plant Physiology, WU): Communication between plants and insects.
  • Prof.dr. C.M.J. Pieterse, Dr. P.A.H.M. Bakker, Dr. A.C.M. van Wees (Plant-Microbe Interactions, UU): Exploring the immune response of Arabidopsis.
  • Dr. J.M. Raaijmakers (Phytopathology, WU): Molecular and functional analysis of biosurfactant production in beneficial and plant pathogenic Pseudomonas species.
  • Dr. R.C. Schuurink, Prof.dr. M.A. Haring (Plant Physiology, UvA): The role of plant volatiles in airborne communication.
  • Prof. dr. J.J.A. van Loon (Entomology, WU): Ecophysiology of insect-plant interactions.
  • Dr. N.M. van Dam (RU Ecogenomics): Interactions aboveground-belowground induced responses.
  • Prof.dr. M. Dicke (Entomology, WU): Chemical and molecular ecology of tritrophic interactions.
  • Prof.dr. L.E.M. Vet, Prof. W.H. van der Putten, Dr. A. Biere (NIOO): Interactions aboveground-belowground induced responses.
  • Dr. M.R. Kant (Population Biology, UvA): Exploring how herbivore variability leads to adaptation against host-plant defenses.
  • Dr. K. Vrieling, Prof.dr. P.G.L. Klinkhamer (Ecology and Phytochemistry, LU): Ecology and evolution of herbivory and plant defence systems. 

Graduate School Experimental Plant Sciences