Pathogen-induced recruitment of a beneficial bacterium in wheat

Plants are subjected to diverse stresses throughout their lives. Emerging theoretical framework suggests that they may have co-evolved multiple strategies to cooperate with microorganisms to cope with stresses. However, empirical evidence underlying co-evolution processes and mutualistic plant-microbial interactions in stress scenarios are limited. In this study, we tested the hypothesis that infection by the soil-borne hemi-biotrophic pathogen Fusarium pseudograminearum (Fp), which causes a devastating crown rot disease on wheat, affects the community structure of the wheat-associated microbiome. Rhizosphere and plant samples were collected from a field experiment where durum wheat (Triticum aestivum) was naturally infected with Fp at different levels for individuals. Phylogenetic marker gene sequencing was used to profile microbial communities and evaluate effects of Fp infection on plant microbiomes. Our data revealed that diseased plants were associated with distinct rhizosphere and root endosphere microbiomes compared with healthy plants. We observed that infected plants had higher abundances of some taxa including a beneficial bacterium Stenotrophomonas rhizophila (SR80) in the rhizosphere soil and root endosphere. This bacterium reached 3×10⁸ cfu g^-1 in the rhizosphere soil, accounting for up to 12% of the microbes in the root endosphere. Further analyses revealed that the abundance of SR80 had a positive linear correlation with the Fp load at base stems and expression of defense genes in leaves. We were able to isolate SR80 from the rhizosphere, which upon re-introduction in soils promoted wheat growth, survival rates, and enhanced defense signaling in plant leaves, but only in the presence of the pathogen. This bacterium seems to have acted as an early warning system for plant defense against the Fp. Together, these findings provide novel evidence for the potential protection of plants by a beneficial microbe against pathogens via modulation of the plant immune system.