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Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface

文献类型： 外文期刊

作者： Landry, Zachary C. 1 ; Vergin, Kevin 1 ; Mannenbach, Christopher 1 ; Block, Stephen 1 ; Yang, Qiao 1 ; Blainey, Pau 1 ;

作者机构： 1.Oregon State Univ, Dept Microbiol, Corvallis, OR 97331 USA

2.Swiss Fed Inst Technol, Inst Umweltingenieurwissensch, Zurich, Switzerland

3.Chinese Acad Fishery Sci, East China Sea Fisheries Inst, Shanghai, Peoples R China

4.Broad Inst MIT & Harvard, Dept Biol Engn, Cambridge, MA USA

5.Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA 93106 USA

关键词： single-cellgenomics; E01-9C-26; marine microbiology; microfluidics; optofluidics; bermuda-atlantic; time-series

期刊名称：FRONTIERS IN MICROBIOLOGY （ 影响因子：5.64； 五年影响因子：6.32 ）

ISSN： 1664-302X

年卷期： 2018 年 9 卷

页码：

收录情况： SCI

摘要： Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. Plankton cells were visually selected and manually sorted with an optical trap, yielding 20 partial genome sequences representing seven bacterial phyla. Two organisms, E01-9C-26 (Gammaproteobacteria), represented by four single cell genomes, and Opi. OSU. 00C, an uncharacterized Verrucomicrobia, were the first of their types retrieved by single cell genome sequencing and were studied in detail. Metagenomic data showed that E01-9C-26 is found throughout the dark ocean, while Opi. OSU. 00C was observed to bloom transiently in the nutrient-depleted euphotic zone of the late spring and early summer. The E01-9C-26 genomes had an estimated size of 4.76-5.05 Mbps, and contained "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes. Metabolic reconstruction indicated E01-9C-26 are likely versatile methylotrophs capable of scavenging C1 compounds, methylated compounds, reduced sulfur compounds, and a wide range of amines, including D-amino acids. The genome sequences identified E01-9C-26 as a source of "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes, but are of unknown function. In contrast, Opi. OSU. 00C genomes encode genes for catabolizing carbohydrate compounds normally associated with eukaryotic phytoplankton. This exploration of optofluidics showed that it was effective for retrieving diverse single-cell bacterioplankton genomes and has potential advantages in microbiology applications that require working with small sample volumes or targeting cells by their morphology.

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