Results

Controlled foliar infection triggered substantial, cultivar-specific shifts in rhizosphere communities across two successive generations. Despite the number of differentially abundant ASVs detected being ten times higher in the second generation than in the first one, the same taxonomic groups were involved in the shifts: Burkholderiales, Flavobacteriales, and Bacillales. Furthermore, the communities linked to the susceptible cultivar consistently shifted more strongly upon infection than the communities linked to the resistant cultivar. The obtained ASV sequences were used to identify 163 corresponding isolates through sequence alignment. Their inhibition potential against P. infestans sporangia and zoospores was assessed through biological assays. These revealed the biocontrol potential of genera otherwise not yet known to inhibit phytopathogenic organisms, such as Advenella, Nocardioides and Phyllobacterium strains. Although we found no correlation between the relative abundance shift of the ASVs upon infection and the activity of the corresponding strains, we observed that the overall activity of strains isolated from the resistant cultivar was higher than that of the strains isolated from the susceptible one.

Conclusion

Taken together, the higher activity of the strains isolated from the resistant cultivar, along with its comparatively modest microbiome shifts upon infection suggest that the investigated resistant cultivar might harbour specific microbiota enriched in strains that are able to inhibit pathogen development and possibly contribute to its higher resistance against P. infestans.

https://link.springer.com/article/10.1186/s40793-026-00910-x

A new publication with the FRIC affiliation from Prof. Laure Weisskopf's group.