Raman‐activated cell sorting and metagenomic sequencing revealing carbon‐fixing bacteria in the ocean. (2nd July 2018)

• Record Type: Journal Article
• Authors: Jing, Xiaoyan; Gou, Honglei; Gong, Yanhai; Su, Xiaolu; Xu, La; Ji, Yuetong; Song, Yizhi; Thompson, Ian P.; Xu, Jian; Huang, Wei E.
• Is Part Of: Environmental microbiology. Volume 20:Number 6(2018)
• Page Start: 2241
• Page End: 2255
• Publication Date: 2018-07-02
• Subjects: Microbial ecology -- Periodicals; Environmental Microbiology -- Periodicals; 579.17
• DOI: 10.1111/1462-2920.14268
• Languages: English
• ISSNs: 1462-2912

Abstract

Summary: 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 13 C 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 13 C 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 .