Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment

Abstract

The subseafloor marine biosphere may be one of the largest reservoirs of microbial biomass on Earth and has recently been the subject of debate in terms of the composition of its microbial inhabitants, particularly on sediments from the Peru Margin. A metagenomic analysis was made by using whole-genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment. A total of 61.9 Mb of genetic material was sequenced from sediments at horizons 1, 16, 32, and 50 m below the seafloor. These depths include sediments from both primarily sulfate-reducing methane-generating regions of the sediment column. Many genes of the annotated genes, including those encoding ribosomal proteins, corresponded to those from the Chloroflexi and Euryarchaeota. However, analysis of the 16S small-subunit ribosomal genes suggests that Crenarchaeota are the abundant microbial member. Quantitative PCR confirms that uncultivated Crenarchaeota are indeed a major microbial group in these subsurface samples. These findings show that the marine subsurface is a distinct microbial habitat and is different from environments studied by metagenomics, especially because of the predominance of uncultivated archaeal groups.

Fig. 1.

Phylogenetic identities of the BLASTX hits to metagenome against the protein nonredundant database. Shown are the percentages of the total of identifiable hits (1 original, n = 14,341; 1 amplified, n = 14,176; 16 mbsf, n = 7,670; 32 mbsf, n = 11,267; 50 mbsf, n = 11,889).

Fig. 2.

Phylogenetic identities, based on matches to Pfam entries for 24 ribosomal proteins (detailed in Table S1). Shown are the percentages of the total of identifiable hits (1 original, n = 107; 1 amplified, n = 79; 16 mbsf, n = 65; 32 mbsf, n = 97; 50 mbsf, n = 130).

Fig. 3.

Phylogenetic groups of subsurface metagenome, based on 16S rRNA homologous gene fragments. Shown are the percentages of the total of identifiable hits (1 original, n = 39; 1 amplified, n = 18; 16 mbsf, n = 56; 32 mbsf, n = 65; 50 mbsf, n = 17).

Fig. 4.

Quantitative PCR data from original and amplified sediment DNAs. Crenarchaeota (771F/957R) are shown as circles, Bacteria (519F/907R) are shown as squares. Original DNAs are open symbols, RepliG amplified DNAs are filled symbols. Each data point represents the average of multiple measurements, with the standard deviation of measurements shown as error. The archaeal results have been graphed with a 0.5-m offset to distinguish data points.