Revealing CO 2 -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 2 -fixing genes, pathways, and chassis from the oceans. Here, we investigated CO 2 -fixing microbes in seawater from the euphotic zone of the Yellow Sea of China by detecting and tracking their 13 C-bicarbonate ( 13 C-HCO 3 - ) 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 Pelagibacter spp., which actively assimilates 13 C-HCO 3 - , and also possesses most of the genes encoding enzymes of the Calvin-Benson cycle for CO 2 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 Pelagibacter spp. were confirmed by heterologous expression in E. coli . These results suggest that hitherto uncultured Pelagibacter spp. uses light-powered metabolism to contribute to global carbon cycling.