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...
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ftdoajarticles:oai:doaj.org/article:27edcef369fd44bd9c535ef4ad449ad4 2023-05-15T17:45:44+02:00 Assembling the marine metagenome, one cell at a time. Tanja Woyke Gary Xie Alex Copeland José M González Cliff Han Hajnalka Kiss Jimmy H Saw Pavel Senin Chi Yang Sourav Chatterji Jan-Fang Cheng Jonathan A Eisen Michael E Sieracki Ramunas Stepanauskas 2009-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0005299 https://doaj.org/article/27edcef369fd44bd9c535ef4ad449ad4 EN eng Public Library of Science (PLoS) https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19390573/pdf/?tool=EBI https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0005299 https://doaj.org/article/27edcef369fd44bd9c535ef4ad449ad4 PLoS ONE, Vol 4, Iss 4, p e5299 (2009) Medicine R Science Q article 2009 ftdoajarticles https://doi.org/10.1371/journal.pone.0005299 2022-12-31T09:00:18Z 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. ... Article in Journal/Newspaper Northwest Atlantic Directory of Open Access Journals: DOAJ Articles PLoS ONE 4 4 e5299 |
institution |
Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Medicine R Science Q |
spellingShingle |
Medicine R Science Q Tanja Woyke Gary Xie Alex Copeland José M González Cliff Han Hajnalka Kiss Jimmy H Saw Pavel Senin Chi Yang Sourav Chatterji Jan-Fang Cheng Jonathan A Eisen Michael E Sieracki Ramunas Stepanauskas Assembling the marine metagenome, one cell at a time. |
topic_facet |
Medicine R Science Q |
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 |
Article in Journal/Newspaper |
author |
Tanja Woyke Gary Xie Alex Copeland José M González Cliff Han Hajnalka Kiss Jimmy H Saw Pavel Senin Chi Yang Sourav Chatterji Jan-Fang Cheng Jonathan A Eisen Michael E Sieracki Ramunas Stepanauskas |
author_facet |
Tanja Woyke Gary Xie Alex Copeland José M González Cliff Han Hajnalka Kiss Jimmy H Saw Pavel Senin Chi Yang Sourav Chatterji Jan-Fang Cheng Jonathan A Eisen Michael E Sieracki Ramunas Stepanauskas |
author_sort |
Tanja Woyke |
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 (PLoS) |
publishDate |
2009 |
url |
https://doi.org/10.1371/journal.pone.0005299 https://doaj.org/article/27edcef369fd44bd9c535ef4ad449ad4 |
genre |
Northwest Atlantic |
genre_facet |
Northwest Atlantic |
op_source |
PLoS ONE, Vol 4, Iss 4, p e5299 (2009) |
op_relation |
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19390573/pdf/?tool=EBI https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0005299 https://doaj.org/article/27edcef369fd44bd9c535ef4ad449ad4 |
op_doi |
https://doi.org/10.1371/journal.pone.0005299 |
container_title |
PLoS ONE |
container_volume |
4 |
container_issue |
4 |
container_start_page |
e5299 |
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1766148958624677888 |