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bioRxiv · 10.64898/2026.05.12.724390

Metagenomics-enabled proteomics reveals how AMF and PSB co-inoculation reshapes tomato rhizosphere dynamics across growth stages

Son, Y.·Craft, E. J.·Pineros, M. A.·Mathieson, O. L.·Awan, A.·Blakeley-Ruiz, J. A.·Kleiner, M.·Kao-Kniffin, J.
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Abstract

Urban agriculture increasingly relies on compost-based substrates for sustainable production, yet we lack a clear characterization of how these systems respond to biological amendments aimed at introducing beneficial microbiota. Here we investigated how developmental stage and co-inoculation with arbuscular mycorrhizal fungi (AMF) and phosphate-solubilizing bacteria (PSB) reshape rhizosphere microbial function in Solanum lycopersicum grown in compost-based urban farm substrate. Using plant physiology assays, 16S rRNA amplicon sequencing, and metagenome-informed metaproteomics, we characterized tomato physiological responses and rhizosphere microbial activity during flowering and fruiting across control, single AMF, single PSB, and AMF and PSB co-inoculation treatments. Co-inoculation synergistically enriched beneficial taxa, improved fruit nutrient accumulation, elevated nutrient transporter and quorum sensing protein production, and drove stress-driven dormancy in competitively excluded taxa, with responses varying between developmental stages. Our findings establish metagenome-informed metaproteomics as essential for resolving stage-specific rhizosphere microbiome functional responses to tomato development and AMF and PSB co-inoculation.

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Son, Y., Craft, E. J., Pineros, M. A., Mathieson, O. L., Awan, A., Blakeley-Ruiz, J. A., Kleiner, M., Kao-Kniffin, J.. 2026-05-13. Metagenomics-enabled proteomics reveals how AMF and PSB co-inoculation reshapes tomato rhizosphere dynamics across growth stages. https://doi.org/10.64898/2026.05.12.724390

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