Assembling the Marine Metagenome, One Cell at a Time
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...
Published in: | PLoS ONE |
---|---|
Main Authors: | , , , , , , , , , , , , , |
Format: | Text |
Language: | English |
Published: |
Public Library of Science
2009
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668756 http://www.ncbi.nlm.nih.gov/pubmed/19390573 https://doi.org/10.1371/journal.pone.0005299 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:2668756 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:2668756 2023-05-15T17:45:43+02:00 Assembling the Marine Metagenome, One Cell at a Time Woyke, Tanja Xie, Gary Copeland, Alex González, José 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 2009-04-23 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668756 http://www.ncbi.nlm.nih.gov/pubmed/19390573 https://doi.org/10.1371/journal.pone.0005299 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668756 http://www.ncbi.nlm.nih.gov/pubmed/19390573 http://dx.doi.org/10.1371/journal.pone.0005299 Woyke et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2009 ftpubmed https://doi.org/10.1371/journal.pone.0005299 2013-09-02T12:16:50Z 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. ... Text Northwest Atlantic PubMed Central (PMC) PLoS ONE 4 4 e5299 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Research Article |
spellingShingle |
Research Article Woyke, Tanja Xie, Gary Copeland, Alex González, José 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 Assembling the Marine Metagenome, One Cell at a Time |
topic_facet |
Research Article |
description |
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. ... |
format |
Text |
author |
Woyke, Tanja Xie, Gary Copeland, Alex González, José 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 |
author_facet |
Woyke, Tanja Xie, Gary Copeland, Alex González, José 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 |
author_sort |
Woyke, Tanja |
title |
Assembling the Marine Metagenome, One Cell at a Time |
title_short |
Assembling the Marine Metagenome, One Cell at a Time |
title_full |
Assembling the Marine Metagenome, One Cell at a Time |
title_fullStr |
Assembling the Marine Metagenome, One Cell at a Time |
title_full_unstemmed |
Assembling the Marine Metagenome, One Cell at a Time |
title_sort |
assembling the marine metagenome, one cell at a time |
publisher |
Public Library of Science |
publishDate |
2009 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668756 http://www.ncbi.nlm.nih.gov/pubmed/19390573 https://doi.org/10.1371/journal.pone.0005299 |
genre |
Northwest Atlantic |
genre_facet |
Northwest Atlantic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668756 http://www.ncbi.nlm.nih.gov/pubmed/19390573 http://dx.doi.org/10.1371/journal.pone.0005299 |
op_rights |
Woyke et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0005299 |
container_title |
PLoS ONE |
container_volume |
4 |
container_issue |
4 |
container_start_page |
e5299 |
_version_ |
1766148933064589312 |