Synthetic rhizosphere bacterial communities induce systemic resistance to barley powdery mildew without major shifts in the native bacterial community

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Rigerte, Linda ; Sommer, Anna ; Vlot, A. Corina ; Prada-Salcedo, Luis Daniel ; Reitz, Thomas ; Heintz-Buschart, Anna ; Tarkka, Mika T.:
Synthetic rhizosphere bacterial communities induce systemic resistance to barley powdery mildew without major shifts in the native bacterial community.
In: Frontiers in Microbiology. Bd. 17 (2026) . - 1818676.
ISSN 1664-302X
DOI: https://doi.org/10.3389/fmicb.2026.1818676

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Abstract

Introduction:
Synthetic microbial communities (SynComs) could help plants withstand biotic stress and reduce the need for pesticides. However, it remains unclear whether SynComs composed of host- or non-host-associated rhizosphere bacteria can trigger induced systemic resistance (ISR) in barley without causing major shifts in the native rhizosphere bacterial community.

Methods:
Here, we constructed two SynComs with known strain composition, composed of bacterial strains isolated from the host-associated barley rhizosphere and non-host-associated wheat rhizosphere. Their ability to trigger induced systemic resistance (ISR) against the barley powdery mildew pathogen Blumeria graminis f. sp. hordei (Bgh) was tested. To investigate plant-microbe interactions from both plant and microbial perspectives, we quantified Bgh propagation in leaves by DAF staining, analysed leaf transcriptomes, and profiled the rhizosphere microbiome using 16S rRNA gene amplicon sequencing and metatranscriptomics.

Results:
Both SynComs reduced fungal growth in barley leaves to a similar extent as the positive control strain, Pseudomonas simiae WCS417r, suggesting that ISR-like protection can also be achieved by defined multi-strain communities. Although both SynComs provided similar overall protection, the barley SynCom exhibited the strongest numerical reduction in fungal growth. These findings build on previous single-strain ISR studies and suggest that community-mediated protection is not restricted to host-derived bacterial consortia. Inoculations with both SynComs and WCS417r were not associated with statistically significant changes in the rhizosphere bacterial community structure. All treatments induced only subtle pre-infection transcriptional responses in barley leaves that were consistent with ISR-mediated priming. However, treatment with WCS417r yielded a higher number of differentially expressed genes than either SynCom. Rhizosphere metatranscriptomics revealed treatment-specific functional shifts. The two features K05516 and PF02868 were affected by all three treatments, implying the existence of shared changes related to stress adaptation and microbial activity. OTUs matching the inoculated SynCom members were still present in the rhizosphere at harvest, suggesting the persistence of at least some of the introduced communities.

Conclusion:
Together, these findings suggest that SynCom-based ISR is potentially a more ecologically relevant approach to microbiome-mediated disease protection in barley.