Vaccinating the microbiota of plants, a new approach to biological control

During the next three years, the research groups of Prof. Weisskopf and Dr Falquet of the Department of Biology of the University of Fribourg will be working hand in hand on a very innovative project, funded at CHF 410,000 by the Gebert Rüf Foundation. The purpose of the project is to replace chemical fungicides by bacteria naturally selected by the plants themselves to combat the pathogens which attack them.

Potato blight is a disease caused by Phytophthora infestans, a destructive pathogenic agent which mainly develops during warm, damp weather. Found all over the world, this disease is the main enemy in  potato cultivation and also attacks tomatoes. It can survive in the soil from one year to the next or be introduced by contaminated plants, so it is very difficult to eradicate. In fact, once there is an outbreak of the disease, overcoming it involves repeated and expensive chemical treatments, while an inappropriate attempt to control it can result in considerable economic damage right up to complete loss of production.

Biological control vs pesticides to protect our ecosystem
Thanks to biological control techniques based on the mechanisms which govern the interactions between species in the natural world, the current trend in research is the detection of antagonistic microorganisms which will attack pathogenic agents. These microorganisms, in this case bacteria naturally associated with the plants one is trying to protect, are normally selected in a controlled manner. Laure Weisskopf, Professor of the Department of Biology, explains: «We mostly select the bacteria ourselves on the basis of their effectiveness in laboratory tests.» But that may well change in the future. The plants, she argues, are able to adapt their microbiota themselves in case of attack by a pathogen and she goes on to say: «it has been discovered that the plant is naturally capable of using its roots to specifically attract certain protective bacteria in order to defend itself against disease. This is quite new and until now has only been demonstrated in a model laboratory plant». This novel premise – the plant knows better what is needed than we do – was the starting point for the research project of this microbiologist and her bioinformatician colleague.

High-throughput sequencing, a state-of-the-art technology in the service of science
In order to stimulate the plant’s natural selection of beneficial bacteria, the researchers are going to expose the potato plants to small doses of the disease. They will then extract the DNA of the entire bacterial microbiota of the plants inoculated in this way and analyse it in comparison to that of control plants which have not been inoculated. This is where Dr Falquet, who is also a researcher in the Department of Biology and group leader of the Swiss Institute of Bioinformatics, comes in. Thanks to his expertise in new high-throughput sequencing technologies, this analysis of the impact of the disease on the composition of the microbiota of the plant can be done faster and at a lower cost. And this is invaluable when one considers that such new biological control solutions do not come onto the market as fast as the chemical products disappear. The aim is now to extract and isolate the bacteria identified in this way as being selected by the plant itself and to test their protective effect by inoculating them on new generations of potatoes. The test will be carried out in the greenhouse, but also on small plots of land thanks to a third project partner, Dr Dupuis of Agroscope Changins.

The Gebert Rüf foundation promotes innovation for the benefit of Switzerland’s economy and society. Its aim is to support application and outcome-oriented science projects carried out at Swiss universities.

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