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.

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