Environmental genome shotgun sequencing of the Sargasso Sea.
We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.
Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA. jcventer@tcag.org
J Craig
JC
Venter
Karin
K
Remington
John F
JF
Heidelberg
Aaron L
AL
Halpern
Doug
D
Rusch
Jonathan A
JA
Eisen
Dongying
D
Wu
Ian
I
Paulsen
Karen E
KE
Nelson
William
W
Nelson
Derrick E
DE
Fouts
Samuel
S
Levy
Anthony H
AH
Knap
Michael W
MW
Lomas
Ken
K
Nealson
Owen
O
White
Jeremy
J
Peterson
Jeff
J
Hoffman
Rachel
R
Parsons
Holly
H
Baden-Tillson
Cynthia
C
Pfannkoch
Yu-Hui
YH
Rogers
Hamilton O
HO
Smith
D001105:Archaea / Q000235:genetics*; D001267:Atlantic Ocean; D001419:Bacteria / Q000235:genetics*; D001435:Bacteriophages / Q000235:genetics; D044822:Biodiversity; D019295:Computational Biology; D000458:Cyanobacteria / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D017753:Ecosystem; D005057:Eukaryotic Cells; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D020459:Genes, rRNA; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics; D008969:Molecular Sequence Data; D010788:Photosynthesis; D010802:Phylogeny; D010957:Plasmids; D012243:Rhodopsin / Q000235:genetics; D025604:Rhodopsins, Microbial; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D014871:Water Microbiology
D025604:Rhodopsins, Microbial; C413548:proteorhodopsin; D012243:Rhodopsin