Early seed priming with closely related Bacillus strains induces divergent physiological and defense responses in melon

Abstract

Early microbial seed priming is conceived to improve crop resilience, yet it remains unclear whether plants can discriminate among closely related beneficial strains and integrate dose-dependent microbial cues. We primed melon ( Cucumis melo) seeds with two phylogenetically similar Bacillus strains ( Bacillus subtilis NCIB3610 and B. velezensis FZB42) and combined transcriptomic, metabolomic, and physiological analyses across development. Despite comparable colonization, the strains provoked contrasting host programs and distinct dose responses. B. subtilis promoted radicle elongation, chloroplastic starch storage, and drought tolerance regardless of inoculum level, together with L-tryptophan and palatinose accumulation. By contrast, B. velezensis displayed a clear dose effect: low inoculum sustained normal radicle growth, whereas high inoculum transiently repressed it, coinciding with suppression of allene oxide synthase, genes related to proteasome complex, and enrichment of flavonoids and glutathione in leaves. Chemical assays showed that radicle inhibition depends on the synergistic action of surfactin, produced by both strains, and bacillomycin D, an iturin-type lipopeptide specific to FZB42. This synergy explains the strain-specific lipopeptide repertoire to the dose-dependent growth response. Although their early trajectories diverged, both primings converged on enhanced aboveground stress resilience. 3610-primed plants restricted Botrytis cinerea via caffeic and rosmarinic acid accumulation, whereas FZB42-primed plants curtailed jasmonate-sensitive Tetranychus urticae mites through jasmonic acid pathway modulation. Our results demonstrate that melon perceives inoculum dose and microbial identity, translating them into distinct metabolic and defense programs that converge on stress resilience. These mechanistic insights (linking lipopeptide fingerprints, sentinel metabolites, and defense transcripts) provide a framework for precision seed treatments in horticultural crops.

Acknowledgements

We thank Saray Morales for providing technical support. We also thank Cristina Lucena-Serrano, Gregorio Martín-Caballero, and Adolfo Martínez-Orellana for providing technical support on TEM and SEM analysis (SCAI-UMA). This work was supported by grants from ERC Starting Grant (BacBio 637971), Ministerio de Economía y Competitividad I + D + i Plan Nacional (PID2022-141664NB-I00) and Junta de Andalucía, Proyectos de Investigación, Desarrollo e Innovación (I + D + i) (P20_00479). L.C.-R. is funded by an FPI contract (PRE2022-000585) from Ministerio de Ciencia, Innovación y Universidades. C.M.S. is funded by Agencia Estatal de Investigación (CNS2022-135744). Funding for open access charge: Universidad de Málaga / CBUA.

Author contributions

D.R. conceived the study, and drafted and edited the text; L.C.-R. conceived the study, collected most of the experimental data, performed computational analysis, and drafted the manuscript; C.M.-S. designed, collected, and analyzed the MS data, and edited the manuscript; M.V.B.-C. collected the experimental data and edited the text; D.P. collected the MS data and edited the text; J.H. performed extraction and analysis of lipopeptides; M.P. and M.B.-A. designed and supervised imaging analysis and substantially edited the manuscript; J.M.-A. designed and supervised herbivore assays and edited the text; A.d.V. substantially revised and edited the text; P.C.D. substantially revised and edited the text.

Data availability

All the raw RNA-seq data have been submitted to the Gene Expression Omnibus (GEO) and can be accessed through GEO series accession GSE299630. Metabolomics data are deposited at https://massive.ucsd.edu/ with identifier MSV000098118. All data are available within this article and its supporting information.

Conflicts of interest statement

P.C.D. is an advisor and holds equity in Cybele, BileOmix, and Sirenas, and is a scientific co-founder and advisor, and holds equity and/or received income from Ometa, Enveda, and Arome with prior approval by UC San Diego. P.C.D. also consulted for DSM Animal Health in 2023.

Supplementary material

Supplementary material is available at Horticulture Research online.

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