Phosphate-solubilizing bacteria (PSB) are crucial for enhancing phosphorus bioavailability and regulating phosphorus transformation processes. However, the in situ phosphorus-solubilizing activity and the link between phenotypes and genotypes for PSB remain unidentified. Here we employed single-cell Raman spectroscopy combined with heavy water to discern and quantify soil active PSB. Our results reveal that PSB abundance and in situ activity differed significantly between soil types and fertilization treatments. Inorganic fertilizer input was the key driver for active PSB distribution. Targeted single-cell sorting and metagenomic sequencing of active PSB uncovered several low-abundance genera that are easily overlooked within bulk soil microbiota. We elucidate the underlying functional genes and metabolic pathway, and the interplay between phosphorus and carbon cycling involved in high phosphorus solubilization activity. Our study provides a single-cell approach to exploring PSB from native environments, enabling the development of a microbial solution for the efficient agronomic use of phosphorus and mitigating the phosphorus crisis.

解磷细菌（PSB）对于提高磷的生物利用度和调节磷的转化过程至关重要。然而，PSB 的原位解磷活性以及表型和基因型之间的联系仍不清楚。在这里，我们采用单细胞拉曼光谱结合重水来识别和量化土壤活性 PSB。我们的结果表明，PSB 丰度和原位活性在土壤类型和施肥处理之间存在显着差异。无机肥投入是积极的 PSB 分配的关键驱动力。对活性 PSB 进行靶向单细胞分选和宏基因组测序发现了一些在大量土壤微生物群中很容易被忽视的低丰度属。我们阐明了潜在的功能基因和代谢途径，以及参与高磷溶解活性的磷和碳循环之间的相互作用。我们的研究提供了一种从原生环境中探索 PSB 的单细胞方法，从而能够开发出一种微生物解决方案，以有效地利用磷并缓解磷危机。