Raman-activated cell sorting and metagenomic sequencing revealing carbon-fixing bacteria in the ocean

Journal article

It is of great significance to understand CO2 fixation in the oceans. Using single cell Raman spectra SCRS) as biochemical profiles, Raman activated cell ejection (RACE) was able to link phenotypes and genotypes of cells. Here we show that mini-metagenomic sequences from RACE can be used as a reference to reconstruct nearly complete genomes of key functional bacteria by binning shotgun metagenomic sequencing data. By applying this approach to 13C-bicarbonate spiked seawater from euphotic zone of the Yellow Sea of China, the dominant bacteria Synechococcus spp. and Pelagibacter spp. were revealed, and both of them contain carotenoid and were able to incorporate 13C into the cells at the same time. Genetic analysis of the reconstructed genomes suggests that both Synechococcus spp. and Pelagibacter spp. contained all genes necessary for carotenoid synthesis, light energy harvesting and CO2 fixation. Interestingly, the reconstructed genome indicates that Pelagibacter spp. harbored intact sets of genes for β-carotene (precursor of retional), proteorhodopsin synthesis and anaplerotic CO2 fixation. This novel approach shines light on the role of marine “microbial dark matter” in global carbon cycling, by linking yet-to-be-cultured Synechococcus spp. and Pelagibacter spp. to carbon fixation and flow activities in situ.

Authors: Jing, X; Gou, H; Gong, Y; Su, X; Xu, L

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Wiley
• Journal: Environmental Microbiology
• Volume: 20
• Issue: 6
• Pages: 2241-2255
• Publication date: 2018-05-04
• Acceptance date: 2018-05-01
• DOI: 10.1111/1462-2920.14268
• ISSN: 1462-2912 and 1462-2920
• Keywords: genomics; CO2 fixation; uncultured microbes; proteorhodopsin; stable isotope probing; cell sorting; Raman