Revealing CO-Fixing SAR11 Bacteria in the Ocean by Raman-Based Single-Cell Metabolic Profiling and Genomics.

The majority of marine microbes remain uncultured, which hinders the identification and mining of CO-fixing genes, pathways, and chassis from the oceans. Here, we investigated CO-fixing microbes in seawater from the euphotic zone of the Yellow Sea of China by detecting and tracking their C-bicarbonate (C-HCO) intake via single-cell Raman spectra (SCRS) analysis. The target cells were then isolated by Raman-activated Gravity-driven Encapsulation (RAGE), and their genomes were amplified and sequenced at one-cell resolution. The single-cell metabolism, phenotype and genome are consistent. We identified a not-yet-cultured spp., which actively assimilates C-HCO, and also possesses most of the genes encoding enzymes of the Calvin-Benson cycle for CO fixation, a complete gene set for a rhodopsin-based light-harvesting system, and the full genes necessary for carotenoid synthesis. The four proteorhodopsin (PR) genes identified in the spp. were confirmed by heterologous expression in . These results suggest that hitherto uncultured spp. uses light-powered metabolism to contribute to global carbon cycling.