The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.

Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metageno...

Descripción completa

Guardado en:
Detalles Bibliográficos
Autores principales: Shannon J Williamson, Douglas B Rusch, Shibu Yooseph, Aaron L Halpern, Karla B Heidelberg, John I Glass, Cynthia Andrews-Pfannkoch, Douglas Fadrosh, Christopher S Miller, Granger Sutton, Marvin Frazier, J Craig Venter
Formato: article
Lenguaje:EN
Publicado: Public Library of Science (PLoS) 2008
Materias:
R
Q
Acceso en línea:https://doaj.org/article/4c4384918bda451fb554ccf8199f9595
Etiquetas: Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
id oai:doaj.org-article:4c4384918bda451fb554ccf8199f9595
record_format dspace
spelling oai:doaj.org-article:4c4384918bda451fb554ccf8199f95952021-11-25T06:13:37ZThe Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.1932-620310.1371/journal.pone.0001456https://doaj.org/article/4c4384918bda451fb554ccf8199f95952008-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18213365/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral sequences within microbial fractions, the prevalence of genes among viral sequences that encode microbial physiological function and their distinct phylogenetic distribution lend strong support to the notion that viral-mediated gene acquisition is a common and ongoing mechanism for generating microbial diversity in the marine environment.Shannon J WilliamsonDouglas B RuschShibu YoosephAaron L HalpernKarla B HeidelbergJohn I GlassCynthia Andrews-PfannkochDouglas FadroshChristopher S MillerGranger SuttonMarvin FrazierJ Craig VenterPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 1, p e1456 (2008)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Shannon J Williamson
Douglas B Rusch
Shibu Yooseph
Aaron L Halpern
Karla B Heidelberg
John I Glass
Cynthia Andrews-Pfannkoch
Douglas Fadrosh
Christopher S Miller
Granger Sutton
Marvin Frazier
J Craig Venter
The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.
description Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral sequences within microbial fractions, the prevalence of genes among viral sequences that encode microbial physiological function and their distinct phylogenetic distribution lend strong support to the notion that viral-mediated gene acquisition is a common and ongoing mechanism for generating microbial diversity in the marine environment.
format article
author Shannon J Williamson
Douglas B Rusch
Shibu Yooseph
Aaron L Halpern
Karla B Heidelberg
John I Glass
Cynthia Andrews-Pfannkoch
Douglas Fadrosh
Christopher S Miller
Granger Sutton
Marvin Frazier
J Craig Venter
author_facet Shannon J Williamson
Douglas B Rusch
Shibu Yooseph
Aaron L Halpern
Karla B Heidelberg
John I Glass
Cynthia Andrews-Pfannkoch
Douglas Fadrosh
Christopher S Miller
Granger Sutton
Marvin Frazier
J Craig Venter
author_sort Shannon J Williamson
title The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.
title_short The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.
title_full The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.
title_fullStr The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.
title_full_unstemmed The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.
title_sort sorcerer ii global ocean sampling expedition: metagenomic characterization of viruses within aquatic microbial samples.
publisher Public Library of Science (PLoS)
publishDate 2008
url https://doaj.org/article/4c4384918bda451fb554ccf8199f9595
work_keys_str_mv AT shannonjwilliamson thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT douglasbrusch thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT shibuyooseph thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT aaronlhalpern thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT karlabheidelberg thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT johniglass thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT cynthiaandrewspfannkoch thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT douglasfadrosh thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT christophersmiller thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT grangersutton thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT marvinfrazier thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT jcraigventer thesorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT shannonjwilliamson sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT douglasbrusch sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT shibuyooseph sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT aaronlhalpern sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT karlabheidelberg sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT johniglass sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT cynthiaandrewspfannkoch sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT douglasfadrosh sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT christophersmiller sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT grangersutton sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT marvinfrazier sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
AT jcraigventer sorcereriiglobaloceansamplingexpeditionmetagenomiccharacterizationofviruseswithinaquaticmicrobialsamples
_version_ 1718413980221833216