Assembling The Marine Metagenome, One Cell At A Time

Journal Article · Tue Jan 01 04:00:00 EST 2008 · Science

OSTI ID:960666

Xie, Gang ^[1]; Han, Shunsheng ^[1]; Kiss, Hajnalka ^[1]; Saw, Jimmy ^[1]; Senin, Pavel ^[1]; Woyke, Tanja ^[2]; Copeland, Alex ^[3]; Gonzalez, Jose ^[4]; Chatterji, Sourav ^[3]; Cheng, Jan - Fang ^[3]; Eisen, Jonathan A ^[5]; Sieracki, Michael E ^[6]; Stepanauskas, Ramunas ^[7]

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1. Los Alamos National Laboratory
2. DOE JOINT GENOME INAT.
3. DOE JOINT GENSOME INST.
4. UNIV OF LAGUNA, SPAIN
5. DOE JOINT GENOME INST.
6. UNIV OF CA-DAVIS
7. BIGELOW LAB

The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91% and 78%, respectively. Only 0.24% of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.

• Research Organization: Los Alamos National Laboratory (LANL)
• Sponsoring Organization: DOE
• DOE Contract Number: AC52-06NA25396
• OSTI ID: 960666
• Report Number(s): LA-UR-08-05792; LA-UR-08-5792
• Journal Information: Science, Journal Name: Science; ISSN 0193-4511; ISSN SCEHDK
• Country of Publication: United States
• Language: English

Related Subjects

08 HYDROGEN
ABUNDANCE
AMPLIFICATION
CONTIGS
CULTIVATION
DISTRIBUTION
DNA
DNA SEQUENCING
GENES
GULF OF MAINE
HUMAN POPULATIONS
HYDROGEN
MBP
MICROORGANISMS
NUCLEOTIDES
OXIDATION
PLANKTON
SAMPLING
SEAS
SHORES
SORTING