Single-Cell Profiling Reveals Hidden Drivers of Sediment Phosphorus Release

As external phosphorus inputs are progressively brought under control, microbe-mediated release of legacy phosphorus from sediments to the overlying waters has become a primary contributor to persistent eutrophication and recurrent algal blooms in global freshwater ecosystems. However, inherent challenges exist in capturing the in situ metabolic activity of phosphorus-solubilizing bacteria (PSB) due to intrinsic cultivation biases and the disconnect between bulk metagenomic profiles and the functions of viable cells. Furthermore, a lack of research into the coupling the phenotypic activity and adaptive genetic strategies of PSB in heterogeneous sedimentary environments has led to limited understanding of the mechanisms underlying endogenous phosphorus release. Here, using single-cell Raman spectroscopy coupled with deuterium oxide labeling (Raman-D2O), distinct in situ phosphorus-solubilizing activities of PSB inhabiting eutrophic, mesotrophic, and oligotrophic sediments were quantified. Inorganic PSB dominated in all sediment types but exhibited the highest activity in nutrient-rich eutrophic sites. Their activities correlated strongly with phosphorus speciation and release fluxes at the sediment–water interface of their habits. In contrast, organic PSB prevailed in oligotrophic sediments. Raman-activated cell sorting conbined with metagenomic sequencing uncovered that low-abundance taxa (e.g., Bacillus and Acinetobacter ) acted as disproportionate drivers of phosphorus mobilization. PSB from eutrophic sediments were enriched in genes encoding phosphatases and organic acid hydrolysis pathways, whereas their oligotrophic counterparts favored genes related to high-affinity transporters and polyphosphate storage. These findings elucidate how nutrient regimes shape PSB metabolic traits, advancing mechanistic insights into microbial phosphorus dynamics in aquatic ecosystems and providing a theoretical basis for optimizing lake management strategies to mitigate endogenous pollutant-driven eutrophication risks.