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