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

Xiaoyan Jing; Yanhai Gong; Teng Xu; Paul A Davison; Craig MacGregor-Chatwin; C Neil Hunter; La Xu; Yu Meng; Yuetong Ji; Bo Ma; Jian Xu; Wei E Huang

doi:10.34133/2022/9782712

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

Biodes Res. 2022 Oct 13:2022:9782712. doi: 10.34133/2022/9782712. eCollection 2022.

Authors

Xiaoyan Jing^{1

2

3}, Yanhai Gong^{1

3}, Teng Xu^{1

3}, Paul A Davison⁴, Craig MacGregor-Chatwin⁴, C Neil Hunter⁴, La Xu⁵, Yu Meng^{1

3}, Yuetong Ji^{1

3

6}, Bo Ma^{1

3}, Jian Xu^{1

2

3}, Wei E Huang⁷

Affiliations

¹ Single-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.
² Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China.
³ University of Chinese Academy of Sciences, Beijing, China.
⁴ Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK.
⁵ Disease and Fishery Drugs Research Center, Marine Biology Institute of Shandong Province, Qingdao, ShandongChina.
⁶ Single-Cell Biotechnology, Ltd, Qingdao, ShandongChina.
⁷ Department 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.