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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ftosti:oai:osti.gov:960666 2023-07-30T04:05:54+02:00 Assembling The Marine Metagenome, One Cell At A Time Xie, Gang Han, Shunsheng Kiss, Hajnalka Saw, Jimmy Senin, Pavel Woyke, Tanja Copeland, Alex Gonzalez, Jose Chatterji, Sourav Cheng, Jan - Fang Eisen, Jonathan A Sieracki, Michael E Stepanauskas, Ramunas 2021-02-12 application/pdf http://www.osti.gov/servlets/purl/960666 https://www.osti.gov/biblio/960666 unknown http://www.osti.gov/servlets/purl/960666 https://www.osti.gov/biblio/960666 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 2021 ftosti 2023-07-11T08:47:26Z 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. ... Other/Unknown Material Northwest Atlantic SciTec Connect (Office of Scientific and Technical Information - OSTI, U.S. Department of Energy) |
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SciTec Connect (Office of Scientific and Technical Information - OSTI, U.S. Department of Energy) |
op_collection_id |
ftosti |
language |
unknown |
topic |
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 |
spellingShingle |
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 Xie, Gang Han, Shunsheng Kiss, Hajnalka Saw, Jimmy Senin, Pavel Woyke, Tanja Copeland, Alex Gonzalez, Jose Chatterji, Sourav Cheng, Jan - Fang Eisen, Jonathan A Sieracki, Michael E Stepanauskas, Ramunas Assembling The Marine Metagenome, One Cell At A Time |
topic_facet |
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 |
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. ... |
author |
Xie, Gang Han, Shunsheng Kiss, Hajnalka Saw, Jimmy Senin, Pavel Woyke, Tanja Copeland, Alex Gonzalez, Jose Chatterji, Sourav Cheng, Jan - Fang Eisen, Jonathan A Sieracki, Michael E Stepanauskas, Ramunas |
author_facet |
Xie, Gang Han, Shunsheng Kiss, Hajnalka Saw, Jimmy Senin, Pavel Woyke, Tanja Copeland, Alex Gonzalez, Jose Chatterji, Sourav Cheng, Jan - Fang Eisen, Jonathan A Sieracki, Michael E Stepanauskas, Ramunas |
author_sort |
Xie, Gang |
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 |
publishDate |
2021 |
url |
http://www.osti.gov/servlets/purl/960666 https://www.osti.gov/biblio/960666 |
genre |
Northwest Atlantic |
genre_facet |
Northwest Atlantic |
op_relation |
http://www.osti.gov/servlets/purl/960666 https://www.osti.gov/biblio/960666 |
_version_ |
1772818211498098688 |