Single‐cell Raman and functional gene analyses reveal microbial P solubilization in agriculture waste‐modified soils

• Published in: mLife 2023-06, Vol.2 (2), p.190-200
• Main Authors: Li, Hongzhe, Ding, Jiazhi, Zhu, Longji, Xu, Fei, Li, Wenjing, Yao, Yanpo, Cui, Li
• Format: Article
• Language: English
• Subjects: Agricultural production; Bacteria; CNP functional genes; D2O isotope labeling; Enzymes; Fertilizers; Genes; Metabolism; Mineralization; Nutrients; Original Research; phosphate‐solubilizing microorganisms; single‐cell Raman; Soil microorganisms; Spectrum analysis; Sustainable agriculture
• ISSN: 2770-100X; 2097-1699; 2770-100X
• DOI: 10.1002/mlf2.12053

Application of agricultural waste such as rapeseed meal (RM) is regarded as a sustainable way to improve soil phosphorus (P) availability by direct nutrient supply and stimulation of native phosphate‐solubilizing microorganisms (PSMs) in soils. However, exploration of the in situ microbial P solubilizing function in soils remains a challenge. Here, by applying both phenotype‐based single‐cell Raman with D2O labeling (Raman‐D2O) and genotype‐based high‐throughput chips targeting carbon, nitrogen and P (CNP) functional genes, the effect of RM application on microbial P solubilization in three typical farmland soils was investigated. The abundances of PSMs increased in two alkaline soils after RM application identified by single‐cell Raman D2O. RM application reduced the diversity of bacterial communities and increased the abundance of a few bacteria with reported P solubilization function. Genotypic analysis indicated that RM addition generally increased the relative abundance of CNP functional genes. A correlation analysis of the abundance of active PSMs with the abundance of soil microbes or functional genes was carried out to decipher the linkage between the phenotype and genotype of PSMs. Myxococcota and C degradation genes were found to potentially contribute to the enhanced microbial P release following RM application. This work provides important new insights into the in situ function of soil PSMs. It will lead to better harnessing of agricultural waste to mobilize soil legacy P and mitigate the P crisis. Impact statement Stimulation of native soil microorganisms to release soil P stocks is a sustainable means of agricultural production, but faces a major challenge in terms of the deciphering of in situ microbial phosphorus (P) solubilization functions. In this study, single‐cell Raman spectroscopy and carbon, nitrogen and P (CNP) functional gene chips were used to reveal the phenotypes and genotypes of microbial P solubilization function in three farmland soils amended with agricultural waste of rapeseed meal (RM). Effects of RM on soil properties, active phosphate‐solubilizing bacteria, and CNP functional genes that may contribute to P solubilization were revealed, providing important insights into the use of agricultural waste to improve P utilization efficiency.