Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.
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 pre...
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2014
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oai:doaj.org-article:1eae9707ab354e088bc39ce5a90d02502021-11-18T08:16:01ZCore microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.1932-620310.1371/journal.pone.0097338https://doaj.org/article/1eae9707ab354e088bc39ce5a90d02502014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24921648/?tool=EBIhttps://doaj.org/toc/1932-6203Metagenomics-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.Ari J S FerreiraRania SiamJoão C SetubalAhmed MoustafaAhmed SayedFelipe S ChambergoAdam S DaweMohamed A GhazyHazem SharafAmged OufIntikhab AlamAlyaa M Abdel-HaleemHeikki LehvaslaihoEman RamadanAndré AntunesUlrich StinglJohn A C ArcherBoris R JankovicMitchell SoginVladimir B BajicHamza El-DorryPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 6, p e97338 (2014) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Ari J S Ferreira Rania Siam João C Setubal Ahmed Moustafa Ahmed Sayed Felipe S Chambergo Adam S Dawe Mohamed A Ghazy Hazem Sharaf Amged Ouf Intikhab Alam Alyaa M Abdel-Haleem Heikki Lehvaslaiho Eman Ramadan André Antunes Ulrich Stingl John A C Archer Boris R Jankovic Mitchell Sogin Vladimir B Bajic Hamza El-Dorry Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. |
| description |
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. |
| format |
article |
| author |
Ari J S Ferreira Rania Siam João C Setubal Ahmed Moustafa Ahmed Sayed Felipe S Chambergo Adam S Dawe Mohamed A Ghazy Hazem Sharaf Amged Ouf Intikhab Alam Alyaa M Abdel-Haleem Heikki Lehvaslaiho Eman Ramadan André Antunes Ulrich Stingl John A C Archer Boris R Jankovic Mitchell Sogin Vladimir B Bajic Hamza El-Dorry |
| author_facet |
Ari J S Ferreira Rania Siam João C Setubal Ahmed Moustafa Ahmed Sayed Felipe S Chambergo Adam S Dawe Mohamed A Ghazy Hazem Sharaf Amged Ouf Intikhab Alam Alyaa M Abdel-Haleem Heikki Lehvaslaiho Eman Ramadan André Antunes Ulrich Stingl John A C Archer Boris R Jankovic Mitchell Sogin Vladimir B Bajic Hamza El-Dorry |
| author_sort |
Ari J S Ferreira |
| title |
Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. |
| title_short |
Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. |
| title_full |
Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. |
| title_fullStr |
Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. |
| title_full_unstemmed |
Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. |
| title_sort |
core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2014 |
| url |
https://doaj.org/article/1eae9707ab354e088bc39ce5a90d0250 |
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