Integrated mineralogical, metabolomic, and gene expression analysis of the phosphate-solubilizing mechanism of Pseudomonas sp. PSB-13

Phosphate-solubilizing microorganisms (PSMs) are pivotal for soil phosphorus (P) cycling and sustainable agriculture. This study aims to screen a high-efficiency PSM and systematically decipher its solubilization mechanisms for tricalcium phosphate (Ca-P), iron phosphate (Fe-P), and aluminum phosphate (Al-P). PSMs were screened on Pikovskaya (PVK) medium with tricalcium phosphate as the sole P source. The highly efficient strain was identified via 16S rRNA gene sequencing, and its ability to solubilize Ca-P, Fe-P, and Al-P was quantified in liquid culture. Mineralogical alterations were characterized using scanning electron microscopy with energy dispersive spectroscopy (SEM-EDS), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). Exometabolite profiles and the expression of phosphate-solubilizing-related genes were analyzed by untargeted metabolomics and reverse transcription quantitative PCR (RT-qPCR), respectively. Results showed that PSB-13 was identified as Pseudomonas sp., with the highest solubilizing capacity for Ca-P (268.64 mg L⁻¹), followed by Fe-P (38.97 mg L⁻¹) and Al-P (20.09 mg L⁻¹). Mineralogical characterization (SEM-EDS, XRD, FTIR) provided direct evidence of surface erosion, elemental composition changes, and structural alterations on all three phosphates after bacterial treatment. Untargeted metabolomics indicated glutathione metabolism and pyrimidine metabolism were significantly enriched in all insoluble phosphate treatments; key organic acids included malonic acid/lactobionic acid (Ca-P), malonic acid/maleamic acid (Fe-P), and glutamic acid and L-histidine (Al-P). RT-qPCR showed upregulated expression of genes related to organic acid production. The substrate-specific secretion of organic acids and associated gene upregulation in Pseudomonas sp. PSB-13 elucidate a robust phosphate-solubilizing mechanism that supports its application as a phosphate-mobilizing microbial inoculant.