Research Article | Open Access

Volume 2022 |Article ID 9782712 | https://doi.org/10.34133/2022/9782712

Revealing CO2-Fixing SAR11 Bacteria in the Ocean by Raman-Based Single-Cell Metabolic Profiling and Genomics

Xiaoyan Jing,^1,2,3 Yanhai Gong,^1,3 Teng Xu,^1,3 Paul A. Davison,⁴ Craig MacGregor-Chatwin,⁴ C. Neil Hunter,⁴ La Xu,⁵ Yu Meng,^1,3 Yuetong Ji,^1,3,6 Bo Ma,^1,3 Jian Xu ,^1,2,3 and Wei E. Huang ⁷

¹Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
²Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
³University of Chinese Academy of Sciences, Beijing, China
⁴Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
⁵Disease and Fishery Drugs Research Center, Marine Biology Institute of Shandong Province, Qingdao, Shandong, China
⁶Single-Cell Biotechnology, Ltd, Qingdao, Shandong, China
⁷Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, UK

Abstract

The majority of marine microbes remain uncultured, which hinders the identification and mining of CO2-fixing genes, pathways, and chassis from the oceans. Here, we investigated CO2-fixing microbes in seawater from the euphotic zone of the Yellow Sea of China by detecting and tracking their 13C-bicarbonate (13C-HCO3-) 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 13C-HCO3-, and also possesses most of the genes encoding enzymes of the Calvin-Benson cycle for CO2 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.