Endophytic Pseudomonas isolates elicit genotype-dependent resistance-, tolerance-, and susceptibility-associated responses in the wheat-flag smut pathosystem.

Flag smut (FS), caused by Urocystis tritici, remains difficult to manage, and little is known about how endophytic bacteria influence the balance between resistance and tolerance across diverse wheat genotypes. Although endophytic bacteria are increasingly explored as sustainable disease-management tools, their effects on FS outcomes and grain yield remain poorly understood. Here, we evaluated two endophytic Pseudomonas sp. strains (8-2 and 58-1-1), originally isolated from healthy winter wheat plants, for their capacity to modify FS incidence and grain yield across 14 winter wheat varieties spanning a wide range of intrinsic resistance. Seed inoculation enhanced aboveground growth in the tested variety, but disease incidence and grain yield responses varied markedly among genotypes. In most varieties, bacterial inoculation reduced FS incidence and increased grain yield, consistent with resistance-associated outcomes. In contrast, several host-strain combinations exhibited unchanged or increased disease incidence while maintaining or improving yield, indicating tolerance-associated responses. A smaller subset showed increased disease incidence accompanied by yield loss, revealing genotype-specific susceptibility outcomes. Together, these results demonstrate that the two Pseudomonas sp. strains do not uniformly suppress FS but instead differentially shape host responses to infection in a host genotype-dependent manner, giving rise to distinct resistance-, tolerance-, and susceptibility-associated phenotypes. Recognizing these distinct response phenotypes is essential for evaluating endophytic bacteria as agents of FS management.