title: Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.
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.
authors.affiliation: Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.
authors.forename: Ari J S
authors.initials: AJ
authors.lastname: Ferreira
authors.affiliation: Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.
authors.forename: Rania
authors.initials: R
authors.lastname: Siam
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: João C
authors.initials: JC
authors.lastname: Setubal
authors.affiliation: Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Moustafa
authors.affiliation: Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Sayed
authors.affiliation: Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Felipe S
authors.initials: FS
authors.lastname: Chambergo
authors.affiliation: Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
authors.forename: Adam S
authors.initials: AS
authors.lastname: Dawe
authors.affiliation: Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.
authors.forename: Mohamed A
authors.initials: MA
authors.lastname: Ghazy
authors.affiliation: Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.
authors.forename: Hazem
authors.initials: H
authors.lastname: Sharaf
authors.affiliation: Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.
authors.forename: Amged
authors.initials: A
authors.lastname: Ouf
authors.affiliation: Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
authors.forename: Intikhab
authors.initials: I
authors.lastname: Alam
authors.affiliation: Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.
authors.forename: Alyaa M
authors.initials: AM
authors.lastname: Abdel-Haleem
authors.affiliation: Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
authors.forename: Heikki
authors.initials: H
authors.lastname: Lehvaslaiho
authors.affiliation: Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.
authors.forename: Eman
authors.initials: E
authors.lastname: Ramadan
authors.affiliation: Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Portugal.
authors.forename: André
authors.initials: A
authors.lastname: Antunes
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Stingl
authors.affiliation: Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
authors.forename: John A C
authors.initials: JA
authors.lastname: Archer
authors.affiliation: Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
authors.forename: Boris R
authors.initials: BR
authors.lastname: Jankovic
authors.affiliation: Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America.
authors.forename: Mitchell
authors.initials: M
authors.lastname: Sogin
authors.affiliation: Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
authors.affiliation: Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, Cairo, New Cairo, Egypt.
authors.forename: Hamza
authors.initials: H
authors.lastname: El-Dorry
mesh_terms: D000222:Adaptation, Physiological; D008027:Light; D054892:Metagenome; D064307:Microbiota / Q000235:genetics* / Q000502:physiology; D005810:Multigene Family; D010802:Phylogeny; D012623:Seawater / Q000382:microbiology*