Breeding of microbiomes conferring salt tolerance to plants

Pereira, C. G.; Edwards, J. A.; Khasanova, A.; Carlson, A. L.; Brisson, V.; Schaefer, E.; Glavina del Rio, T.; Tringe, S.; Vogel, J. P.; Des Marais, D. L.; Juenger, T. E.; Mueller, U. G.

doi:10.1101/2025.01.13.632835

bioRxiv · 10.1101/2025.01.13.632835

Breeding of microbiomes conferring salt tolerance to plants

Pereira, C. G.·Edwards, J. A.·Khasanova, A.·Carlson, A. L.·Brisson, V.·Schaefer, E.·Glavina del Rio, T.·Tringe, S.·Vogel, J. P.·Des Marais, D. L.·Juenger, T. E.·Mueller, U. G.

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Abstract

Microbiome breeding by host-mediated selection is a technique to artificially select for microbiomes conferring benefits to plants. Here, we describe leaf ionomics, microbial community composition, and network analyses of a microbiome-breeding experiment to generate microbiomes conferring salt tolerance to Brachypodium distachyon, a model for cereal crops. Plants receiving microbiomes selected to confer tolerance to either sodium- or aluminium-stress produced 69-198% higher total seed weight than plants receiving control microbiomes. Sodium-selected microbiomes reduced leaf-sodium concentration by 50%, whereas aluminium-selected microbiomes had no effect on leaf-tissue nutrient concentration, suggesting different mechanisms underlying microbiome-mediated salt tolerance. By testing these selected microbiomes in a cross-fostering experiment, we show that artificially-selected microbiomes attain (a) ecological robustness contributing to transplantability (inheritance) of microbiome-encoded effects between plants; and (b) network features identifying key bacteria promoting stress tolerance. Combined, these findings elucidate critical mechanisms underlying host-mediated selection as a tool to breed beneficial microbiomes in an agricultural context.

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Pereira, C. G., Edwards, J. A., Khasanova, A., Carlson, A. L., Brisson, V., Schaefer, E., Glavina del Rio, T., Tringe, S., Vogel, J. P., Des Marais, D. L., Juenger, T. E., Mueller, U. G.. 2025-01-16. Breeding of microbiomes conferring salt tolerance to plants. https://doi.org/10.1101/2025.01.13.632835

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