Assembling the Marine Metagenome, One Cell at a Time

Journal Article · Thu Jun 24 04:00:00 EDT 2010 · PLoS One

OSTI ID:985325

Woyke, Tanja; Xie, Gary; Copeland, Alex; Gonzalez, Jose M; Han, Cliff; Kiss, Hajnalka; Saw, Jimmy H; Senin, Pavel; Yang, Chi; Chatterji, Sourav; Cheng, Jan-Fang; Eisen, Jonathan A; Sieracki, Michael E; Stepanauskas, Ramunas

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 91percent and 78percent, respectively. Only 0.24percent 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: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: Genomics Division
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 985325
• Report Number(s): LBNL-3661E
• Journal Information: PLoS One, Journal Name: PLoS One
• Country of Publication: United States
• Language: English

Related Subjects

99 GENERAL AND MISCELLANEOUS
ABUNDANCE
AMPLIFICATION
CONTIGS
CULTIVATION
DISTRIBUTION
DNA
DNA SEQUENCING
GENES
GULF OF MAINE
HYDROGEN
MICROORGANISMS
NUCLEOTIDES
OXIDATION
PLANKTON
POTENTIAL ENERGY
QUALITY CONTROL
SAMPLING
SORTING
STRAINS
microbial assemblage
single-cell
sequencing
marine microorganism