Abstract
BackgroundMetagenomics is emerging as a powerful method to study the function and physiology of the unexplored microbial biosphere, and is causing us to re-evaluate basic precepts of microbial ecology and evolution. Most marine metagenomic analyses have been nearly exclusively devoted to photic waters.Methodology/Principal FindingsWe constructed a metagenomic fosmid library from 3,000 m-deep Mediterranean plankton, which is much warmer (∼14°C) than waters of similar depth in open oceans (∼2°C). We analyzed the library both by phylogenetic screening based on 16S rRNA gene amplification from clone pools and by sequencing both insert extremities of ca. 5,000 fosmids. Genome recruitment strategies showed that the majority of high scoring pairs corresponded to genomes from Rhizobiales within the Alphaproteobacteria, Cenarchaeum symbiosum, Planctomycetes, Acidobacteria, Chloroflexi and Gammaproteobacteria. We have found a community structure similar to that found in the aphotic zone of the Pacific. However, the similarities were significantly higher to the mesopelagic (500–700 m deep) in the Pacific than to the single 4000 m deep sample studied at this location. Metabolic genes were mostly related to catabolism, transport and degradation of complex organic molecules, in agreement with a prevalent heterotrophic lifestyle for deep-sea microbes. However, we observed a high percentage of genes encoding dehydrogenases and, among them, cox genes, suggesting that aerobic carbon monoxide oxidation may be important in the deep ocean as an additional energy source.Conclusions/SignificanceThe comparison of metagenomic libraries from the deep Mediterranean and the Pacific ALOHA water column showed that bathypelagic Mediterranean communities resemble more mesopelagic communities in the Pacific, and suggests that, in the absence of light, temperature is a major stratifying factor in the oceanic water column, overriding pressure at least over 4000 m deep. Several chemolithotrophic metabolic pathways could supplement organic matter degradation in this most depleted habitat.
Highlights
The deep ocean is one of the most important and less understood microbial-driven ecosystems on Earth
The only largescale metagenomic analysis of deep-sea communities correspond to a comparative study that DeLong and co-workers carried out at different depths in the water column at the North-Pacific Subtropical Gyre ALOHA station, ranging from 10 to 4,000 m
The Km3 metagenomic library was constructed from planktonic fractions smaller than 5 mm of seawater collected at 3,010 m depth that was at a temperature of nearly 14uC and 38.7% salinity
Summary
The deep ocean is one of the most important and less understood microbial-driven ecosystems on Earth. Since the recognition of the essential role of microbes on the ocean water column [1], most marine microbiology studies have been devoted to the photic zone, where microbial cell density and activity are high and most primary production occurs. The only largescale metagenomic analysis of deep-sea communities correspond to a comparative study that DeLong and co-workers carried out at different depths in the water column at the North-Pacific Subtropical Gyre ALOHA station, ranging from 10 to 4,000 m. The comparison of metagenomic libraries from the deep Mediterranean and the Pacific ALOHA water column showed that bathypelagic Mediterranean communities resemble more mesopelagic communities in the Pacific, and suggests that, in the absence of light, temperature is a major stratifying factor in the oceanic water column, overriding pressure at least over 4000 m deep. Several chemolithotrophic metabolic pathways could supplement organic matter degradation in this most depleted habitat
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