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

Ari J S Ferreira,Amged Ouf,Eman Ramadan,Ulrich Stingl,Mohamed A Ghazy,Hazem Sharaf,Felipe S Chambergo,Vladimir B Bajic,André Antunes,Ahmed Moustafa,Rania Siam,Alyaa M Abdel-Haleem,Ahmed A Sayed ,John Archer ,Intikhab Álam ,Adam Dawe ,Heikki Lehväslaiho ,Boris R Janković ,João Carlos Setúbal ,Mitchell L Sogin ,Hamza A El-Dorry

doi:10.1371/journal.pone.0097338

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.

Highlights

Microbial communities dominate the oceans and seas [1] and are involved in fundamental processes in the global ecosystem, synthesizing half of the photosynthetic biomass and producing significant amounts of oxygen [2]
Acquisition and loss of genetic information, and mutational variation of gene regulatory networks, are known to shape the lifestyles of microorganisms including those that reside in marine environments [18,19,20,21,22,23,24,25]
Defining the reference depth-related environments The metagenomic datasets employed in this work were derived from samples obtained at different sites in the world’s oceans

Summary

Introduction

Microbial communities dominate the oceans and seas [1] and are involved in fundamental processes in the global ecosystem, synthesizing half of the photosynthetic biomass and producing significant amounts of oxygen [2]. To evaluate the effect of low oxygen concentration on the genomic content of microbial communities, COGs that presented statistically significant changes in normalized abundance levels between datasets of the Iquique water column were initially identified following the same procedure performed for the selection of differentially abundant depth-related COGs in the three reference columns (ATII, ALOHA, BATS).

Results

Conclusion