Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

Handle URI:
http://hdl.handle.net/10754/323528
Title:
Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.
Authors:
Ferreira, Ari J S; Siam, Rania; Setubal, João C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehväslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich ( 0000-0002-0684-2597 ) ; Archer, John A.C. ( 0000-0002-3302-3933 ) ; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; El-Dorry, Hamza
Abstract:
Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.
KAUST Department:
Red Sea Research Center (RSRC)
Citation:
Ferreira AJS, Siam R, Setubal JC, Moustafa A, Sayed A, et al. (2014) Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses. PLoS ONE 9: e97338. doi:10.1371/journal.pone.0097338.
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
Issue Date:
12-Jun-2014
DOI:
10.1371/journal.pone.0097338
PubMed ID:
24921648
PubMed Central ID:
PMC4055538
Type:
Article
ISSN:
1932-6203
Additional Links:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0097338; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055538/
Appears in Collections:
Articles; Red Sea Research Center (RSRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorFerreira, Ari J Sen
dc.contributor.authorSiam, Raniaen
dc.contributor.authorSetubal, João Cen
dc.contributor.authorMoustafa, Ahmeden
dc.contributor.authorSayed, Ahmeden
dc.contributor.authorChambergo, Felipe Sen
dc.contributor.authorDawe, Adam Sen
dc.contributor.authorGhazy, Mohamed Aen
dc.contributor.authorSharaf, Hazemen
dc.contributor.authorOuf, Amgeden
dc.contributor.authorAlam, Intikhaben
dc.contributor.authorAbdel-Haleem, Alyaa Men
dc.contributor.authorLehväslaiho, Heikkien
dc.contributor.authorRamadan, Emanen
dc.contributor.authorAntunes, Andréen
dc.contributor.authorStingl, Ulrichen
dc.contributor.authorArcher, John A.C.en
dc.contributor.authorJankovic, Boris Ren
dc.contributor.authorSogin, Mitchellen
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorEl-Dorry, Hamzaen
dc.date.accessioned2014-07-21T10:56:28Z-
dc.date.available2014-07-21T10:56:28Z-
dc.date.issued2014-06-12en
dc.identifier.citationFerreira AJS, Siam R, Setubal JC, Moustafa A, Sayed A, et al. (2014) Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses. PLoS ONE 9: e97338. doi:10.1371/journal.pone.0097338.en
dc.identifier.issn1932-6203en
dc.identifier.pmid24921648en
dc.identifier.doi10.1371/journal.pone.0097338en
dc.identifier.urihttp://hdl.handle.net/10754/323528en
dc.description.abstractMetagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.en
dc.language.isoenen
dc.publisherPublic Library of Science (PLoS)en
dc.relation.urlhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0097338en
dc.relation.urlhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055538/en
dc.rightsArchived with thanks to PloS oneen
dc.titleCore microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.en
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC4055538en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Biology and the Science and Technology Research Center, School of Sciences and Engineering, American University in Cairo, Cairo, New Cairo, Egypten
dc.contributor.institutionDepartamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazilen
dc.contributor.institutionEscola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, Brazilen
dc.contributor.institutionInstitute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Portugalen
dc.contributor.institutionJosephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, United Statesen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorDawe, Adam Seanen
kaust.authorAlam, Intikhaben
kaust.authorLehväslaiho, Heikkien
kaust.authorStingl, Ulrichen
kaust.authorArcher, John A.C.en
kaust.authorBajic, Vladimir B.en
kaust.authorJankovic, Boris R.en

Related articles on PubMed

All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.