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Fig. S1. Neighbor-joining tree indicating the phylogenetic positions of the Gram-positive CVA clones belonging to classes Clostridia, Acidobacteria, Actinobacteria and phyla Nitrospira and Chloroflexi and to Gram-positive unclassified bacteria groups determined by clone library and DGGE analyses from CVA. Sequences in bold are from this study. The scale bar represents 10% nucleotide sequence differences.

Fig. S2. Neighbor-joining tree indicating the phylogenetic positions of the Gram-negative CVA clones belonging to classes Alphaproteobacteria, Betaproteobacteria, Deinococci and Gammaproteobacteria and phylum Bacteroidetes determined by clone library and DGGE analyses from CVA. Sequences in bold are from this study. The scale bar represents 10% nucleotide sequence differences.

Fig. S3. Neighbor-joining tree indicating the phylogenetic positions of the archaeal CVA clones belonging to phylum Euryarchaeota and class Thermoprotei determined by clone library and DGGE analyses from CVA. Sequences in bold are from this study. The scale bar represents 10% nucleotide sequence differences.

Fig. S4. Rarefection curves at a cut-off of 0.05 for: (a) total clones screened (Bacteria •, n = 441; Archaea ○, n = 270) and at cut-off values between 0.01 and 0.1 for (b) total pyrosequences (Bacteria, n = 7897; Archaea, n = 4983).

Fig. S5. Phylogenetic diversity of translated sequences of biotin carboxylase detected in clone library from CVA. CVA sequences are in bold.

Table S1. Primer sets used for detection of genes encoding 16S rRNA SSU for both domains Bacteria and Archaea and genes encoding key enzymes of CO2 metabolic pathways, sulphur and methane cycles.

Table S2. Chemical composition, temperature and pH of the Cabeco de Vide aquifer.

Table S3. Statistical analysis results.

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