Pseudomonas soli C10A8 overcomes iron deficiency in French marigold via a siderophore rich exometabolome

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Iron (Fe) availability is a critical constraint in soilless and hydroponic crop production, where continuous aeration and near-neutral pH promote Fe 2+ oxidation and precipitation, limiting root uptake and inducing interveinal chlorosis. Although synthetic chelates partially mitigate Fe deficiency, their cost and pH-dependent degradation highlight the need for biological alternatives. In this study, we identified siderophore producing bacteria (SPB) that mobilize mineral Fe and mitigate Fe stress in French marigold ( Tagetes patula ‘Durango Yellow’). We screened 1044 greenhouse rhizobacterial isolates using a high-throughput CAS assay and identified 12 top siderophore producers (OD 630 ≤ 0.07). Genome mining via antiSMASH discovered diverse, strain-specific siderophore/metallophore and NRPS biosynthetic gene clusters. Four Pseudomonas strains were evaluated in hydroponics using Hoagland’s (-Fe) solution amended with goethite as the sole Fe source. Digital phenotyping showed inoculum density-dependent (OD 595 = 0.2 vs 0.4) improvements in canopy green hue (90°-180°) for three of four strains, including Pseudomonas soli C10A8, which was selected for further validation. The C10A8 treatment significantly reduced leaf chlorosis and senescence (NPCI, PSRI), increased NDVI, canopy green hue, shoot digital biomass and root biomass relative to the uninoculated control (NC) (p < 0.01 to p < 0.001), and increased shoot Fe concentration (p = 0.031). Untargeted LC–MS/MS metabolomics revealed distinct metabolome separation, with the C10A8 exometabolome enriched in high molecular-weight NRPS-derived features (up to 925-fold). These results identify C10A8 as a PGPR that chelated iron from insoluble goethite (via putative ligand-assisted dissolution) and enhanced French marigold growth, supporting a sustainable microbial alternative to synthetic chelates in controlled environment agriculture.

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