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Fig. S1. Length distribution of (A) reads in the filtered reads dataset from oil reservoir Well I, (B) Well I contigs in the assembled contigs + singletons dataset, (C) reads in the filtered reads dataset from oil reservoir Well II and (D) contigs in the assembled contigs + singletons dataset of Well II.

Fig. S2. Distribution of GC content of reads within the Well II metagenome dataset, plotted as read frequency against GC content (%).

Fig. S3. Comparison of sequences annotated as Methanococcus sp. (left panels), Pelobacter sp. (mid panels) and Thermococcus sp. (right panels) of the metagenome dataset of Well I (upper panels) and Well II (lower panels), to sequences in databases. BLASTn was used in the search and results were plotted as frequency against percent sequence identity.

Fig. S4. Comparison of sequences annotated as Methanococcus (left panel), Pelobacter (mid panel) and Thermococcus (right panel), originating from Well I and Well II. Sequences were analysed by BLASTn search of the respective reads datasets and plotted as read frequency against per cent sequence similarity.

Fig. S5. Sequence analysis of four selected contigs (A–D) annotated as Thermococcus sequences, using BLAST search. Contig sequence regions with best (green) and second best (cyan) species hits as well as other OTU (black) assignments are indicated. Sequence regions annotated to encode CDS (annotated protein, deep blue), tRNA gene sequences (red), rRNA gene sequences (pink) and hypothetical protein-coding sequences (light green/yellow) are also indicated.

Fig. S6. A maximum likelihood phylogenetic tree for six metagenome contig regions (predicted protein sequence of DNA-dependent RNA polymerase) compared with species representing most bacterial phyla. For abbreviations, see Table S2. The source of the metagenome sequences is indicated as W1 (Well I) and W2 (Well II) and their contig serial numbers.

Table S1. Comparison of sequence datasets wells I and II.

Table S2. Species used in phylogenetic analysis.

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