This project addresses the challenge of producing enough food for the increasing world population while at the same time preserving the environment for future generations. Fungal diseases cause enormous yield losses despite the abundant use of hazardous fungicides. Worldwide, consumers’ concerns about pesticide residues in food and environment urge us to find reliable, cost-efficient and environmentally friendly alternatives to our currently used synthetic fungicides. We believe that one such solution lies in harnessing the protective power of the plant microbiome. Like us humans, plants are densely colonized by a large diversity of microbes and the aim of this project is to understand their contribution to plant health, using potato as a model plant and late blight as a model disease. The final goal is to use this plant microbiome understanding to develop new strategies to protect our crops without harming environmental and human health. Transfer of such new strategies to practice shall be done in collaboration with producers’ associations and industrial partners involved in sustainable crop protection.

This project exploits a newly discovered ability of plants to “call for help” and specifically recruit health-protective microbes upon pathogen challenge. Instead of selecting biocontrol agents in artificial laboratory settings, we propose to let the plant select the best microbes itself in a natural enrichment process. Using an unprecedented vaccination-like strategy, we propose to harvest the most active microbiota members selected by the plant upon infection, and to assemble these protective microbiome members in synthetic communities to be applied to new plant generations. The project’s most important intended direct benefit to society will be a lesser reliance on synthetic fungicides, leading to improved environmental and human health. This benefit shall not be restricted to potato production, but once the concept is established, it shall be applied to other staple crops, e.g. wheat, rice or maize, leading to even stronger impact.

The project started in May 2019. Since then, we have performed a large-scale vaccination experiment over three generations using two different potato cultivars, the sensitive cultivar Bintje and the more tolerant cultivar Innovator. While only little changes could be observed after the first vaccination event, the second event led to massive changes in the bacterial community structure, with more than 3’500 different bacteria (detected as amplicon sequence variants, ASVs) whose abundance was either decreased or increased upon vaccination. We focused our attention on the recruited populations and found ca. 170 different ones in our newly isolated collection of over 700 bacterial strains. Functional characterization of these strains in terms of their protective potential against the late blight causing agent revealed that many strains were able to drastically inhibit zoospore release, germination and disease progression in small plants experiments. The protective potential of these new biocontrol agents still needs to be confirmed in the field, but our promising in planta results suggest that at least some of the strains will be suitable for development into eco-friendly and efficient crop protection solution. Before this project started, the “cry for help” hypothesis had only been demonstrated on the model plant Arabidopsis thaliana. Our data now reveal that crop plants such as potato are also very well able to recruit beneficial microbes upon sensing a pathogen attack. This opens the way for a new avenue of plant-protection strategies that could generically be applied to protect different crops from various diseases.

Alfiky A, Abou-Mansour E, De Vrieze M, L' Haridon F & Weisskopf L. 2023. Newly isolated Trichoderma spp. show multifaceted biocontrol strategies to inhibit potato late blight causal agent Phytophthora infestans both in vitro and in planta. Phytobiomes online early.
Dubey S, Anand A, Bhattacharjee A, Khatri S, L'Haridon F, Weisskopf L & Sharma S. 2022. Understanding the mechanism of action of stress-acclimatized rhizospheric microbiome towards salinity stress mitigation in Vigna radiata : A focus on the emission of volatiles. Environmental and Experimental Botany 104988.
Abdelrahman O, Yagi S, El Siddig M, El Hussein A, Germanier F, De Vrieze M, L'Haridon F & Weisskopf L. 2022. Evaluating the Antagonistic Potential of Actinomycete Strains Isolated From Sudan ’ s Soils Against Phytophthora infestans. Frontiers in Microbiology 13: 827824.
Berendsen RL, Vismans G, Yu K, Song Y, De Jonge R, Burgman WP, Burmølle M, Herschend J, Bakker PAHM, Pieterse CMJ. 2018. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J 12:1496– 1507.
De Vrieze, M., Germanier, F., Vuille, N., and Weisskopf, L. 2018. Combining Different Potato-Associated Pseudomonas Strains for Improved Biocontrol of Phytophthora infestans. Front. Microbiol. 9:1–13.
Ritpitakphong U, Falquet L, Vimoltust A, Berger A, Métraux J-PP, L’Haridon F. 2016. The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen. New Phytol 210:1033–1043.

«Faire des bactéries les alliées de la lutte contre le mildiou de la pomme de terre», agrihebdo, 28. January 2022
Pesticides – Qu’une eau pure abreuve nos sillons, café scientifique organized in Fribourg, January 2022
«Der unsichtbare Dschungel unter uns – Alternative für Pestizide», Tages-Anzeiger, 2. Juli 2020
Pour l'auto-défense des plantes contre les pathogènes, RTS, CQFD, 14.5.2019
L'Université de Fribourg veut vacciner des plantes, 20minutes, 10.5.2019
L'Université de Fribourg veut vacciner des plantes, 24heures, 10.5.2019
Stimuler l'autodéfense contre le mildiou, La Liberté, 14.5.2019
L'Université de Fribourg veut vacciner des plantes, TdG, 10.5.2019
Bakterien als Pflanzenmedizin, Schweizer Bauer, 14.5.2019
Mit Bakterien gegen Pflanzenkrankheiten, foodaktuell.ch, 13.5.2019
Un projet pour se passer des fongicides, Agri, 10.5.2019