The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific
Por:
Rusch D.B., Halpern A.L., Sutton G., Heidelberg K.B., Williamson S., Yooseph S., Wu D., Eisen J.A., Hoffman J.M., Remington K., Beeson K., Tran B., Smith H., Baden-Tillson H., Stewart C., Thorpe J., Freeman J., Andrews-Pfannkoch C., Venter J.E., Li K., Kravitz S., Heidelberg J.F., Utterback T., Rogers Y.-H., Falcón L.I., Souza V., Bonilla-Rosso G., Eguiarte L.E., Karl D.M., Sathyendranath S., Platt T., Bermingham E., Gallardo V., Tamayo-Castillo G., Ferrari M.R., Strausberg R.L., Nealson K., Friedman R., Frazier M., Venter J.C.
Publicada:
1 ene 2007
Resumen:
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. © 2007 Rusch et al.
Filiaciones:
Rusch D.B.:
J. Craig Venter Institute, Rockville, MD, United States
Halpern A.L.:
J. Craig Venter Institute, Rockville, MD, United States
Sutton G.:
J. Craig Venter Institute, Rockville, MD, United States
Heidelberg K.B.:
J. Craig Venter Institute, Rockville, MD, United States
Department of Biological Sciences, University of Southern California, Avalon, CA, United States
Williamson S.:
J. Craig Venter Institute, Rockville, MD, United States
Yooseph S.:
J. Craig Venter Institute, Rockville, MD, United States
Wu D.:
J. Craig Venter Institute, Rockville, MD, United States
Genome Center, University of California Davis, Davis, CA, United States
Eisen J.A.:
J. Craig Venter Institute, Rockville, MD, United States
Genome Center, University of California Davis, Davis, CA, United States
Hoffman J.M.:
J. Craig Venter Institute, Rockville, MD, United States
Remington K.:
J. Craig Venter Institute, Rockville, MD, United States
Your Genome, Your World, Rockville, MD, United States
Beeson K.:
J. Craig Venter Institute, Rockville, MD, United States
Tran B.:
J. Craig Venter Institute, Rockville, MD, United States
Smith H.:
J. Craig Venter Institute, Rockville, MD, United States
Baden-Tillson H.:
J. Craig Venter Institute, Rockville, MD, United States
Stewart C.:
J. Craig Venter Institute, Rockville, MD, United States
Thorpe J.:
J. Craig Venter Institute, Rockville, MD, United States
Freeman J.:
J. Craig Venter Institute, Rockville, MD, United States
Andrews-Pfannkoch C.:
J. Craig Venter Institute, Rockville, MD, United States
Venter J.E.:
J. Craig Venter Institute, Rockville, MD, United States
Li K.:
J. Craig Venter Institute, Rockville, MD, United States
Kravitz S.:
J. Craig Venter Institute, Rockville, MD, United States
Heidelberg J.F.:
J. Craig Venter Institute, Rockville, MD, United States
Department of Biological Sciences, University of Southern California, Avalon, CA, United States
Utterback T.:
J. Craig Venter Institute, Rockville, MD, United States
Rogers Y.-H.:
J. Craig Venter Institute, Rockville, MD, United States
Falcón L.I.:
Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
Souza V.:
Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
Bonilla-Rosso G.:
Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
Eguiarte L.E.:
Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
Karl D.M.:
Department of Oceanography, University of Hawaii, Honolulu, HI, United States
Sathyendranath S.:
Bedford Institute of Oceanography, Dartmouth, NS, Canada
Platt T.:
Bedford Institute of Oceanography, Dartmouth, NS, Canada
Bermingham E.:
Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
Gallardo V.:
Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
Tamayo-Castillo G.:
Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica
Ferrari M.R.:
Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, United States
Strausberg R.L.:
J. Craig Venter Institute, Rockville, MD, United States
Nealson K.:
J. Craig Venter Institute, Rockville, MD, United States
Department of Earth Sciences, University of Southern California, Los Angles, CA, United States
Friedman R.:
J. Craig Venter Institute, Rockville, MD, United States
Frazier M.:
J. Craig Venter Institute, Rockville, MD, United States
Venter J.C.:
J. Craig Venter Institute, Rockville, MD, United States
Gold
|