Metagenomics of the Deep Mediterranean, a Warm Bathypelagic Habitat

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.

Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea

“…In contrast, we observed a higher frequency of HGTs involving bacterial donors (31 cases) (Figures 1 and 2). As expected from their high relative abundance in deep-ocean ecosystems Martín-Cuadrado et al, 2007), most of these HGT involved proteobacterial donors but also, and more surprisingly, Firmicutes and Chloroflexi (Figures 3a and b). Although much less frequent than Proteobacteria, both groups are relatively abundant in deep waters of the Mediterranean basin (Martín-Cuadrado et al, 2007;Quaiser et al, 2011).…”

“…As expected from their high relative abundance in deep-ocean ecosystems Martín-Cuadrado et al, 2007), most of these HGT involved proteobacterial donors but also, and more surprisingly, Firmicutes and Chloroflexi (Figures 3a and b). Although much less frequent than Proteobacteria, both groups are relatively abundant in deep waters of the Mediterranean basin (Martín-Cuadrado et al, 2007;Quaiser et al, 2011). These genes of bacterial origin, which are scattered in the genomic fragments analysed (Figure 1), are often shared by a variety of thaumarchaeotal species, including C. symbiosum and N. maritimus, suggesting that the HGT events are ancient.…”

“…Among them, NADH:ubiquinone and Fe-S oxidoreductases in COG category C (energy production and conversion), and amino-acid ABC transporters and carbohydrate transporters (COG categories E and G, amino acid transport and metabolism and carbohydrate transport and conversion) were the most represented. A previous analysis of metagenomic data from the KM3 site showed that transporters, namely amino acid and carbohydrate transporters, are overrepresented in the deep-planktonic community (Martín-Cuadrado et al, 2007), indicating that they are important for living in this nutrientdepleted environment. Because of their functional importance and high frequency, they constitute suitable targets to be involved in HGT events.…”

“…The fact of retrieving Chloroflexi as the second most frequent donor (19 cases, Figures 4b and 5b), in particular in libraries AD1000 and KM3 (10 and 8 cases, respectively), but also in whole fosmid gene phylogenies, might appear more surprising. Nevertheless, as mentioned above, this phylum is relatively abundant in the deep Mediterranean Sea (Martín-Cuadrado et al, 2007;Quaiser et al, 2011), which makes it a likely alternative donor. Other groups (Actinobacteria, Acidobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Planctomycetes and Verrucomicrobia) appeared to have also contributed with several genes to the genomes of planktonic marine archaea (Figures 4b and 5c).…”

“…Bi-directional fosmid-end sequences for 5000 randomly chosen fosmids were already available for the deep-sea plankton metagenomic library KM3 (Ionian Sea, 3000 m depth) (Martín-Cuadrado et al, 2007). We sequenced both ends of 5000 fosmid inserts from each of the two additional metagenomic libraries, SAT1000 (South Atlantic, 1000 m depth) and AD1000 (Adriatic Sea, 1000 m depth).…”