title: The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.
abstract: 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.
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America. DRusch@venterinstitute.org
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Rusch
authors.forename: Aaron L
authors.initials: AL
authors.lastname: Halpern
authors.forename: Granger
authors.initials: G
authors.lastname: Sutton
authors.forename: Karla B
authors.initials: KB
authors.lastname: Heidelberg
authors.forename: Shannon
authors.initials: S
authors.lastname: Williamson
authors.forename: Shibu
authors.initials: S
authors.lastname: Yooseph
authors.forename: Dongying
authors.initials: D
authors.lastname: Wu
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Eisen
authors.forename: Jeff M
authors.initials: JM
authors.lastname: Hoffman
authors.forename: Karin
authors.initials: K
authors.lastname: Remington
authors.forename: Karen
authors.initials: K
authors.lastname: Beeson
authors.forename: Bao
authors.initials: B
authors.lastname: Tran
authors.forename: Hamilton
authors.initials: H
authors.lastname: Smith
authors.forename: Holly
authors.initials: H
authors.lastname: Baden-Tillson
authors.forename: Clare
authors.initials: C
authors.lastname: Stewart
authors.forename: Joyce
authors.initials: J
authors.lastname: Thorpe
authors.forename: Jason
authors.initials: J
authors.lastname: Freeman
authors.forename: Cynthia
authors.initials: C
authors.lastname: Andrews-Pfannkoch
authors.forename: Joseph E
authors.initials: JE
authors.lastname: Venter
authors.forename: Kelvin
authors.initials: K
authors.lastname: Li
authors.forename: Saul
authors.initials: S
authors.lastname: Kravitz
authors.forename: John F
authors.initials: JF
authors.lastname: Heidelberg
authors.forename: Terry
authors.initials: T
authors.lastname: Utterback
authors.forename: Yu-Hui
authors.initials: YH
authors.lastname: Rogers
authors.forename: Luisa I
authors.initials: LI
authors.lastname: Falcón
authors.forename: Valeria
authors.initials: V
authors.lastname: Souza
authors.forename: Germán
authors.initials: G
authors.lastname: Bonilla-Rosso
authors.forename: Luis E
authors.initials: LE
authors.lastname: Eguiarte
authors.forename: David M
authors.initials: DM
authors.lastname: Karl
authors.forename: Shubha
authors.initials: S
authors.lastname: Sathyendranath
authors.forename: Trevor
authors.initials: T
authors.lastname: Platt
authors.forename: Eldredge
authors.initials: E
authors.lastname: Bermingham
authors.forename: Victor
authors.initials: V
authors.lastname: Gallardo
authors.forename: Giselle
authors.initials: G
authors.lastname: Tamayo-Castillo
authors.forename: Michael R
authors.initials: MR
authors.lastname: Ferrari
authors.forename: Robert L
authors.initials: RL
authors.lastname: Strausberg
authors.forename: Kenneth
authors.initials: K
authors.lastname: Nealson
authors.forename: Robert
authors.initials: R
authors.lastname: Friedman
authors.forename: Marvin
authors.initials: M
authors.lastname: Frazier
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
mesh_terms: D019295:Computational Biology; D020387:Food Chain; D009792:Oceans and Seas; D010933:Plankton; D013045:Species Specificity; D014871:Water Microbiology