Revealing CO 2 -Fixing SAR11 Bacteria in the Ocean by Raman-Based Single-Cell Metabolic Profiling and Genomics.
Xiaoyan JingYanhai GongTeng XuPaul A DavisonCraig MacGregor-ChatwinC Neil HunterLa XuYu MengYuetong JiBo MaJian XuWei E HuangPublished in: Biodesign research (2022)
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.
Keyphrases
- single cell
- genome wide
- rna seq
- bioinformatics analysis
- genome wide identification
- high throughput
- dna methylation
- poor prognosis
- induced apoptosis
- escherichia coli
- copy number
- gene expression
- stem cells
- minimally invasive
- mass spectrometry
- raman spectroscopy
- mesenchymal stem cells
- body mass index
- cell proliferation
- long non coding rna
- cell therapy
- signaling pathway