Single-cell exploration of active microbiota in solubilizing fixed phosphorus in soils

Abstract Phosphate solubilizing bacteria (PSB) play a crucial role in mobilizing soil fixed phosphorus (P) and mitigating P crisis. However, it is a grand challenge to reveal their in situ P-solubilizing activity and the link between phenotypes and genotypes. Here, single-cell Raman-D₂O was employed to discern and quantify soil active PSB. Their abundance and in situ activity differed significantly between soil types and fertilization treatments. Inorganic nutrient input was determined as the key driver for active PSB distributions. Further targeted single-cell sorting and metagenome sequencing of highly active soil PSB revealed novel unculturable genera with a low abundance in bulk soil microbiota. The underlying functional genes and metabolic pathway, especially the previously unrecognized interplay between P and C cycling involved in high P solubilization activity, were elucidated. This study provides a new single-cell approach to exploring PSB from native environments, enabling development of microbial solution for sustainable P utilization in agriculture.