A scalable screening approach reveals phylogenetic patterns of bacterial antagonism against potato pathogens

Pichon, V.; Gillon, A.; Ruffieux, G.; Luethi, T.; Morales Undurraga, C.; De Vrieze, M.; L'Haridon, F.; Abdelrahman, O.; Weisskopf, L.

doi:10.64898/2026.09.22.753498

bioRxiv · 10.64898/2026.09.22.753498

A scalable screening approach reveals phylogenetic patterns of bacterial antagonism against potato pathogens

Pichon, V.·Gillon, A.·Ruffieux, G.·Luethi, T.·Morales Undurraga, C.·De Vrieze, M.·L'Haridon, F.·Abdelrahman, O.·Weisskopf, L.

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Abstract

Microbial biological control agents (mBCAs) offer a promising alternative to conventional disease management, but identifying effective strains requires screening large microbial collections against many pathogens. Here, we developed a scalable screening approach to characterize the antagonistic activity of potato-associated bacteria against multiple pathogens and investigated how bacterial origin and phylogeny relate to antagonistic phenotypes. A collection of 600 bacterial strains isolated from two potato cultivars, three plant compartments using four cultivation media was screened against six major potato pathogens: the bacteria Dickeya solani and Pectobacterium carotovorum, the fungi Alternaria solani and Rhizoctonia solani, and the oomycetes Phytophthora infestans and Pythium ultimum. A scalable confrontation method was developed for non-filamentous bacteria, while complementary lower-throughput assays were used for filamentous strains. This approach enabled successful assessment of 92% of non-filamentous and 97% of filamentous strain-pathogen combinations. Isolation cultivar, plant compartment and cultivation medium had only limited effects on the proportion of antagonistic strains. In contrast, pathogen sensitivity varied markedly: P. infestans was the most susceptible pathogen, whereas D. solani and P. carotovorum were generally resistant to bacterial antagonism. Antagonistic activity clustered phylogenetically, with Bacillus and Streptomyces containing many broad-spectrum inhibitors. In addition, several taxa showed preferential activity against the oomycetes, including P. infestans-specific antagonists from the Pseudomonas genus and P. ultimum-specific antagonists from the Frigoribacterium, Curtobacterium, Pedobacter and Phyllobacterium genera. Overall, multi-pathogen screening revealed distinct generalist and specialist antagonistic profiles and identified candidate strains and taxa for further evaluation as mBCAs.

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Pichon, V., Gillon, A., Ruffieux, G., Luethi, T., Morales Undurraga, C., De Vrieze, M., L'Haridon, F., Abdelrahman, O., Weisskopf, L.. 2026-09-23. A scalable screening approach reveals phylogenetic patterns of bacterial antagonism against potato pathogens. https://doi.org/10.64898/2026.09.22.753498

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