VIROME NGS ANALYSIS OF PESTS AND PATHOGENS FOR PLANT PROTECTION (VIROPLANT)
Within this project we look at a special new form of biological crop protection, namely the use of bacteriophages or bacteria-eating viruses, in this case against plant-damaging bacteria. There is a technical and a socio-economic component. In the latter, we examine, among other things, the perception surrounding this crop protection and make a techno-economic analysis (legal provisions? risk analysis? market exploration?). As far as the technical part is concerned, the aim is to find bacteriophages against the rhizogenic bacterium Rhizobium radiobacter, which disrupts the functioning of the roots of tomato and cucumber plants. This is done as follows: The root cells are induced to produce an overproduction of hormones, resulting in excessive root growth ('crazy roots'). The result is reduced fruit setting and fruit formation, and thus loss of production and economic damage. Bacteriophages are able to recognise specific proteins on the cell wall of the rhizogenic bacterium on which they attach themselves like a lunar lander to inject the virus into the bacterial cell. That virus then multiplies in the bacterial cell so that it collapses. The newly formed viruses break out of the bacterial cell and start looking for other rhizogenic bacteria.
The bacteriological part of the examination is carried out by ILVO. We phenotype and genotype a collection of rhizogenic Rhizobium isolates from crazy roots and carrot mat of tomato and cucumber crops in Flanders. Typing these isolates is crucial because not every isolate produces crazy roots to the same extent. For genotyping we use sequences (with NGS -next generation sequencing). We determine the biological reaction of each type of isolate to the plant by measuring the root mass and seeing to what extent the plant becomes diseased. This information is of great importance in the selection of effective phages, which attack those isolates that are strong causes of crazy root disease. Then it becomes possible to compose phage cocktails. We perform tests with the cocktails as a pesticide, in bioassays. For the techno-economic analysis a multi-actor case study approach will be used. Within representative cases, different socio-economic topics will be investigated in close collaboration with different relevant stakeholders. Considering PESTLE logic, system thinking and business model design, the input of the stakeholders needed to perform the different tasks will be collected through both qualitative (e.g. interviews and focus groups) and quantitative (e.g. choice experiments) methods.
Crazy roots mainly occur in the substrate cultivation of tomatoes and cucumbers, which means that less and less oxygen is present in the substrate. The bacterium also forms a biofilm within the irrigation system of a greenhouse. This makes them more resistant to antibacterial substances and therefore more difficult to remove and control. Different chemical and/or biological solutions exist to control the infection pressure. A disadvantage of chemical disinfection is the possible formation of toxic by-products that are harmful to humans and the environment. And the treatment also kills beneficial micro-organisms around the plant roots. The biological solutions we are aiming for in this research are promising. The use of phages within the agricultural sector is pioneering work. It involves a radically new strategy to combat bacterial plant diseases. We expect it to be more sustainable than the use of natural enemies (antagonists) that inhibit the bacterium but do not kill it. The researchers expect that they will be able to take at least a few steps towards an efficient phage cocktail or one super phage. This is a big step forward for the recognition of biological crop protection products.