Potato foliar infection with Phytophthora infestans drives strong, cultivar-specific shifts in rhizosphere communities

Potato is an important crop worldwide, yet its production is severely threatened by Phytophthora infestans, the causal agent of late blight. Alternatives to the current control strategies are needed, as these rely heavily on environmentally harmful treatments. The recruitment of beneficial microbes by plants upon stress (“cry-for-help” mechanism) may represent an opportunity to find new biocontrol agents but this has not yet been reported for potato. The aim of this study was to analyse whether foliar late blight infection induces shifts in the phyllosphere, rhizosphere and soil bacterial communities associated with two potato cultivars of differing sensitivity to late blight. Moreover, we aimed at isolating plant microbiota members to test whether bacteria putatively recruited upon infection would be particularly active in protecting the plant against late blight.

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.

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.