Phyllosphere Bacterial Communities in Wheat and Faba Bean Intercropping: Structural and Functional Mechanisms in Response to Stripe Rust Infection

Crop microbiome-phyllosphere interactions are vital for intercropping disease control. Although evidence suggests that intercropping enhances nutrient efficiency and recruits beneficial bacteria at the root-soil interface, limited research has explored changes in the phyllosphere microbiome in response to foliar diseases. Pot experiments were conducted to investigate how wheat stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst), affects shoot biomass, total nitrogen, and total potassium content; changes of phyllosphere bacteria; co-occurrence networks; and ecological functions in wheat and faba bean intercropping using 16S amplicon sequencing. Microbial characterization revealed that Pst infection altered the phyllosphere bacteria of wheat and faba bean, reducing evenness and richness, shifting community structure with the emergence of new bacteria, and weakening microbial networks under both planting patterns. Compared with monocropping, intercropping displayed bacterial features of an integrated system, fortified wheat community diversity with new bacteria such as Pseudomonas aeruginosa in wheat and Pantoea and Burkholderia in faba bean, and strengthened the bacterial network of wheat in response to Pst infection. Intercropping enhanced nitrogen and carbon cycling in wheat leaves by improving nitrite respiration and aromatic hydrocarbon degradation. The enriched phyllosphere bacterial structure positively correlated with the crop's performance by balancing shoot biomass, nitrogen, and potassium accumulation between wheat and faba bean upon Pst infection to mitigate the disease index of wheat. Overall, these changes may positively correlate with functions aiding wheat in suppressing wheat stripe rust. The findings provide new insight into understanding how intercropping improves response to pathogen challenge as an effective planting practice. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .