Revealing CO2-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<sub>2</sub>-fixing genes, pathways, and chassis from the oceans. Here, we investigated CO<sub>2</sub>-fixing microbes in seawater from the euphotic zone of the Yellow Sea of C...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
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American Association for the Advancement of Science
2022
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| _version_ | 1826311888434102272 |
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| author | Jing, X Gong, Y Xu, T Davison, PA MacGregor-Chatwin, C Hunter, CN Xu, L Meng, Y Ji, Y Ma, B Xu, J Huang, WE |
| author_facet | Jing, X Gong, Y Xu, T Davison, PA MacGregor-Chatwin, C Hunter, CN Xu, L Meng, Y Ji, Y Ma, B Xu, J Huang, WE |
| author_sort | Jing, X |
| collection | OXFORD |
| description | The majority of marine microbes remain uncultured, which hinders the identification and mining of CO<sub>2</sub>-fixing genes, pathways, and chassis from the oceans. Here, we investigated CO<sub>2</sub>-fixing microbes in seawater from the euphotic zone of the Yellow Sea of China by detecting and tracking their <sup>13</sup>C-bicarbonate (<sup>13</sup>C-HCO<sub>3</sub><sup>-</sup>) 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 <i>Pelagibacter</i> spp., which actively assimilates <sup>13</sup>C-HCO<sub>3</sub><sup>-</sup>, and also possesses most of the genes encoding enzymes of the Calvin-Benson cycle for CO<sub>2</sub> 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 <i>Pelagibacter</i> spp. were confirmed by heterologous expression in <i>E. coli</i>. These results suggest that hitherto uncultured <i>Pelagibacter</i> spp. uses light-powered metabolism to contribute to global carbon cycling. |
| first_indexed | 2024-03-07T08:17:54Z |
| format | Journal article |
| id | oxford-uuid:ec577b5d-c58f-4f5f-b28e-37529d525404 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T08:17:54Z |
| publishDate | 2022 |
| publisher | American Association for the Advancement of Science |
| record_format | dspace |
| spelling | oxford-uuid:ec577b5d-c58f-4f5f-b28e-37529d5254042024-01-12T14:55:59ZRevealing CO2-fixing SAR11 bacteria in the ocean by Raman-based single-cell metabolic profiling and genomicsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:ec577b5d-c58f-4f5f-b28e-37529d525404EnglishSymplectic ElementsAmerican Association for the Advancement of Science2022Jing, XGong, YXu, TDavison, PAMacGregor-Chatwin, CHunter, CNXu, LMeng, YJi, YMa, BXu, JHuang, WEThe majority of marine microbes remain uncultured, which hinders the identification and mining of CO<sub>2</sub>-fixing genes, pathways, and chassis from the oceans. Here, we investigated CO<sub>2</sub>-fixing microbes in seawater from the euphotic zone of the Yellow Sea of China by detecting and tracking their <sup>13</sup>C-bicarbonate (<sup>13</sup>C-HCO<sub>3</sub><sup>-</sup>) 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 <i>Pelagibacter</i> spp., which actively assimilates <sup>13</sup>C-HCO<sub>3</sub><sup>-</sup>, and also possesses most of the genes encoding enzymes of the Calvin-Benson cycle for CO<sub>2</sub> 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 <i>Pelagibacter</i> spp. were confirmed by heterologous expression in <i>E. coli</i>. These results suggest that hitherto uncultured <i>Pelagibacter</i> spp. uses light-powered metabolism to contribute to global carbon cycling. |
| spellingShingle | Jing, X Gong, Y Xu, T Davison, PA MacGregor-Chatwin, C Hunter, CN Xu, L Meng, Y Ji, Y Ma, B Xu, J Huang, WE Revealing CO2-fixing SAR11 bacteria in the ocean by Raman-based single-cell metabolic profiling and genomics |
| title | Revealing CO2-fixing SAR11 bacteria in the ocean by Raman-based single-cell metabolic profiling and genomics |
| title_full | Revealing CO2-fixing SAR11 bacteria in the ocean by Raman-based single-cell metabolic profiling and genomics |
| title_fullStr | Revealing CO2-fixing SAR11 bacteria in the ocean by Raman-based single-cell metabolic profiling and genomics |
| title_full_unstemmed | Revealing CO2-fixing SAR11 bacteria in the ocean by Raman-based single-cell metabolic profiling and genomics |
| title_short | Revealing CO2-fixing SAR11 bacteria in the ocean by Raman-based single-cell metabolic profiling and genomics |
| title_sort | revealing co2 fixing sar11 bacteria in the ocean by raman based single cell metabolic profiling and genomics |
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