The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorc...
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
---|---|
Format: | Article in Journal/Newspaper |
Language: | unknown |
Published: |
eScholarship, University of California
2007
|
Subjects: | |
Online Access: | https://escholarship.org/uc/item/45f4516d |
id |
ftcdlib:oai:escholarship.org/ark:/13030/qt45f4516d |
---|---|
record_format |
openpolar |
spelling |
ftcdlib:oai:escholarship.org/ark:/13030/qt45f4516d 2023-05-15T17:36:47+02:00 The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. Rusch, Douglas B Halpern, Aaron L Sutton, Granger Heidelberg, Karla B Williamson, Shannon Yooseph, Shibu Wu, Dongying Eisen, Jonathan A Hoffman, Jeff M Remington, Karin Beeson, Karen Tran, Bao Smith, Hamilton Baden-Tillson, Holly Stewart, Clare Thorpe, Joyce Freeman, Jason Andrews-Pfannkoch, Cynthia Venter, Joseph E Li, Kelvin Kravitz, Saul Heidelberg, John F Utterback, Terry Rogers, Yu-Hui Falcón, Luisa I Souza, Valeria Bonilla-Rosso, Germán Eguiarte, Luis E Karl, David M Sathyendranath, Shubha Platt, Trevor Bermingham, Eldredge Gallardo, Victor Tamayo-Castillo, Giselle Ferrari, Michael R Strausberg, Robert L Nealson, Kenneth Friedman, Robert Frazier, Marvin Venter, J Craig e77 2007-03-01 application/pdf https://escholarship.org/uc/item/45f4516d unknown eScholarship, University of California qt45f4516d https://escholarship.org/uc/item/45f4516d public PLoS biology, vol 5, iss 3 Plankton Computational Biology Water Microbiology Food Chain Species Specificity Oceans and Seas Biological Sciences Agricultural and Veterinary Sciences Medical and Health Sciences Developmental Biology article 2007 ftcdlib 2020-11-20T15:17:05Z The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS. Article in Journal/Newspaper North Atlantic Northwest Atlantic University of California: eScholarship Pacific |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Plankton Computational Biology Water Microbiology Food Chain Species Specificity Oceans and Seas Biological Sciences Agricultural and Veterinary Sciences Medical and Health Sciences Developmental Biology |
spellingShingle |
Plankton Computational Biology Water Microbiology Food Chain Species Specificity Oceans and Seas Biological Sciences Agricultural and Veterinary Sciences Medical and Health Sciences Developmental Biology Rusch, Douglas B Halpern, Aaron L Sutton, Granger Heidelberg, Karla B Williamson, Shannon Yooseph, Shibu Wu, Dongying Eisen, Jonathan A Hoffman, Jeff M Remington, Karin Beeson, Karen Tran, Bao Smith, Hamilton Baden-Tillson, Holly Stewart, Clare Thorpe, Joyce Freeman, Jason Andrews-Pfannkoch, Cynthia Venter, Joseph E Li, Kelvin Kravitz, Saul Heidelberg, John F Utterback, Terry Rogers, Yu-Hui Falcón, Luisa I Souza, Valeria Bonilla-Rosso, Germán Eguiarte, Luis E Karl, David M Sathyendranath, Shubha Platt, Trevor Bermingham, Eldredge Gallardo, Victor Tamayo-Castillo, Giselle Ferrari, Michael R Strausberg, Robert L Nealson, Kenneth Friedman, Robert Frazier, Marvin Venter, J Craig The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. |
topic_facet |
Plankton Computational Biology Water Microbiology Food Chain Species Specificity Oceans and Seas Biological Sciences Agricultural and Veterinary Sciences Medical and Health Sciences Developmental Biology |
description |
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS. |
format |
Article in Journal/Newspaper |
author |
Rusch, Douglas B Halpern, Aaron L Sutton, Granger Heidelberg, Karla B Williamson, Shannon Yooseph, Shibu Wu, Dongying Eisen, Jonathan A Hoffman, Jeff M Remington, Karin Beeson, Karen Tran, Bao Smith, Hamilton Baden-Tillson, Holly Stewart, Clare Thorpe, Joyce Freeman, Jason Andrews-Pfannkoch, Cynthia Venter, Joseph E Li, Kelvin Kravitz, Saul Heidelberg, John F Utterback, Terry Rogers, Yu-Hui Falcón, Luisa I Souza, Valeria Bonilla-Rosso, Germán Eguiarte, Luis E Karl, David M Sathyendranath, Shubha Platt, Trevor Bermingham, Eldredge Gallardo, Victor Tamayo-Castillo, Giselle Ferrari, Michael R Strausberg, Robert L Nealson, Kenneth Friedman, Robert Frazier, Marvin Venter, J Craig |
author_facet |
Rusch, Douglas B Halpern, Aaron L Sutton, Granger Heidelberg, Karla B Williamson, Shannon Yooseph, Shibu Wu, Dongying Eisen, Jonathan A Hoffman, Jeff M Remington, Karin Beeson, Karen Tran, Bao Smith, Hamilton Baden-Tillson, Holly Stewart, Clare Thorpe, Joyce Freeman, Jason Andrews-Pfannkoch, Cynthia Venter, Joseph E Li, Kelvin Kravitz, Saul Heidelberg, John F Utterback, Terry Rogers, Yu-Hui Falcón, Luisa I Souza, Valeria Bonilla-Rosso, Germán Eguiarte, Luis E Karl, David M Sathyendranath, Shubha Platt, Trevor Bermingham, Eldredge Gallardo, Victor Tamayo-Castillo, Giselle Ferrari, Michael R Strausberg, Robert L Nealson, Kenneth Friedman, Robert Frazier, Marvin Venter, J Craig |
author_sort |
Rusch, Douglas B |
title |
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. |
title_short |
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. |
title_full |
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. |
title_fullStr |
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. |
title_full_unstemmed |
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. |
title_sort |
sorcerer ii global ocean sampling expedition: northwest atlantic through eastern tropical pacific. |
publisher |
eScholarship, University of California |
publishDate |
2007 |
url |
https://escholarship.org/uc/item/45f4516d |
op_coverage |
e77 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
North Atlantic Northwest Atlantic |
genre_facet |
North Atlantic Northwest Atlantic |
op_source |
PLoS biology, vol 5, iss 3 |
op_relation |
qt45f4516d https://escholarship.org/uc/item/45f4516d |
op_rights |
public |
_version_ |
1766136385413054464 |