Responses of root-associated microorganisms of different drought-tolerant potato varieties to drought conditions

Potato is a globally important food crop, but its growth is highly susceptible to drought stress. Drought not only reduces potato yield but also alters the structure of the rhizosphere microbial community, thereby affecting the plant’s drought tolerance and overall health. In this study, metagenomic sequencing was conducted on the rhizosphere microbiota of the drought-tolerant potato genotype C93 and the drought-sensitive variety Favorita, grown under rain-proof shed soil conditions, to investigate their structural and functional responses under varying drought intensities. The results showed that as drought severity increased, the alpha diversity of Favorita first decreased and then increased, whereas the alpha diversity of C93 remained relatively stable. Proteobacteria (30.44%-63.00%) and Actinobacteria were the dominant phyla across all treatments, but genus-level composition exhibited genotype-specific differences. Under severe drought conditions, C93 enriched <italic>Lysobacter</italic> (10.16%) and <italic>Sphingomonas</italic> (6.37%), while Favorita was dominated by <italic>Nocardia</italic> (8.29%) and <italic>Streptomyces</italic>. Functional annotation revealed that under moderate drought stress, the ABC transporter pathway played a key role in both C93 and Favorita’s responses. However, under severe drought, C93 primarily relied on the ABC transporter pathway, while Favorita depended on the AMPK signaling pathway to mitigate stress. Microbial network analysis further demonstrated that C93 maintained greater network stability through a cooperative interaction model involving a “core microbiota + functional hub”, whereas Favorita exhibited insufficient network modularity and relied on the expansion of single functional taxa, resulting in weaker long-term drought resilience. This study provides preliminary insights into genotype-specific mechanisms by which rhizosphere microorganisms regulate drought resistance in potato, offering a theoretical foundation for the development of drought-tolerant microbial agents and the advancement of drought- resilience technologies.