Multi-omics reveal dual phosphate-solubilizing mechanisms in sugarcane: bacterial gluconic acid secretion and host flavonoid modulation

While conventional phosphorus fertilizer application temporarily meets plant phosphorus demand, its long-term overuse has caused widespread and potentially irreversible ecological damage. Phosphate-solubilizing microorganisms (PSMs) are widely recognized as a sustainable alternative to enhance plant phosphorus acquisition; however, most studies to date have focused on screening PSMs for P-solubilizing traits, while a systematic characterization of the transcriptional and metabolic dynamics in sugarcane following PSM inoculation remains a critical and largely unaddressed knowledge gap. To address this gap, we integrated 16S rRNA amplicon sequencing, plant growth-promoting trait assays, whole-genome analysis of bacterial isolates, host transcriptomics, untargeted metabolomics, rhizosphere microbiome profiling, and soil physicochemical and plant physiological analyses to comprehensively elucidate the mechanisms underlying PSM-mediated phosphorus uptake in sugarcane under varying phosphorus availability. First, through amplicon sequencing of sugarcane rhizosphere samples under high- and low-phosphorus conditions, we identified Gammaproteobacteria and Burkholderiales as core microbial taxa responsive to soil phosphorus levels. We subsequently isolated 21 culturable PSMs from the sugarcane rhizosphere and, after systematic validation of their P-solubilizing and plant growth-promoting traits, narrowed the selection to two elite strains that significantly enhanced sugarcane phosphorus uptake: Burkholderia seminalis Y2 and Pantoea sp. Y20. Functional and genomic analyses revealed that Y20 strain primarily solubilize inorganic phosphorus via gluconic acid secretion. Focusing on the superior strain Y20, we performed integrated multi-omics analyses to elucidate its multifaceted mode of action. Rhizosphere microbiome profiling showed that Y20 inoculation markedly reshaped the sugarcane rhizosphere microbial community, with a significantly increased relative abundance of beneficial genera, including Streptomyces , Lechevalieria , and Mycobacterium . Concurrently, Y20 inoculation substantially improved the rhizosphere phosphorus acquisition microenvironment by increasing soil organic matter and available phosphorus content, enhancing rhizosphere acid phosphatase activity, and ultimately improving key agronomic traits of sugarcane. Crucially, integrated transcriptomic and metabolomic analyses directly addressed the central knowledge gap by demonstrating that Y20 enabled sugarcane to cope with low- phosphorus stress through regulation of flavonoid biosynthesis, circadian rhythm, and genes involved in tropane and piperidine alkaloid biosynthetic pathways. Key flavonoid biosynthesis genes ( CHI , CHS , CYP75B1 , etc.) were significantly upregulated, accompanied by marked increases in phloretin, fustin, luteolin, and other flavonoid metabolites, thereby identifying flavonoid biosynthesis as a central component of the phosphate-solubilizing bacteria (PSB)-mediated phosphorus uptake promotion mechanism. Collectively, this study provides the first systematic characterization of transcriptional and metabolic dynamics in sugarcane following PSB inoculation and, through integrated multi-omics approaches, comprehensively reveals the multidimensional mechanisms by which PSBs facilitate plant phosphorus acquisition. Our findings lay a solid theoretical foundation for the development of sustainable phosphorus management strategies and high-efficiency PSB-based microbial fertilizers for sugarcane production.