Fig. S1. Neighbour-joining phylogeny of all full-length 3% OTU representatives for SPG12 Planktomycetes (A), Chloroflexi (B) and other bacterial phyla (C with SPG12 sequences only; D,E, SPG11 sequences included), based on ∼1200 bp alignments of 16S rRNA sequences. A maximum-composite likelihood substitution model with gamma-corrected site rates was used in MEGA4. Support for clades was estimated by 1000 interior branch test replicates. Three per cent representative phylotypes defined on partial reads for the 153–163 depth layer were not included in phylogenies (Table S2). References for previously defined uncultured clades are as follows: (A) CPla-3, Köhler et al. (2008). (B) SAR202, Giovannoni et al. (1996); SAR202 subclusters, Morris and colleagues (2004); Chloroflexi clades I–IV, Inagaki and colleagues (2006). (C) NKB19, Li and colleagues (1999), Hugenholtz and colleagues (2002); SAR324, Wright and colleagues (1997); Termite Group I, Ohkuma and Kudo (1996); OP8, Hugenholtz and colleagues (1998); NT-B2, Reed and colleagues (2002). (E) SAR11, Giovannoni and colleagues (1990); SARmet-5, Teske and colleagues (2011); JTB255, Li and colleagues (2009). (D) SAR406, Gordon and Giovannoni (1996); WS3, Dojka and colleagues (1998); NT-B9, Reed and colleagues (2002); BRC1, Derakshani et al. (2001).

Fig. S2. Rarefaction analysis at 1% OTU resolution for Archaea (grey symbols) and Bacteria (black symbols).

Table S1. Representative phylotypes for archaea in the SPG12 sediment column, based on 1% OTU definition. The accession number, the best BLAST hit, the phylogenetic classification and the number of clones in different sediment horizons are listed for each phylotype.

Table S2. Representative phylotypes for bacteria in the SPG12 sediment column, based on 3% OTU definition. The accession number, phylogenetic classification and the number of clones in different sediment horizons are listed for each phylotype.

Table S3. Archaeal and bacterial diversity indices for SPG12 clone libraries. Furthest-neighbour diversity analyses for SPG12 Archaea (A) and Bacteria (B) were calculated in MOTHUR (Schloss et al., 2009), using the furthest-neighbour approach and an OTU definition of 3%. For comparative indices, the first row shows the shared Chao1 estimated diversity (Chao, 1984), the second row lists abundance-based Jaccard (Yue et al., 2001) and the third ThetaYC similarity (Yue and Clayton, 2005). Also listed for Bacteria is the Shannon diversity index and the Pielou evenness index, both calculated using phylum as the relevant taxonomic unit.

Table S4. Relative comparison of potential DNA concentrations in PCR reactions, based on sediment cell densities, volume of sediment extracted and volume of PCR extract used per PCR reaction. Three per cent OTU bacterial and 1% OTU archaeal Chao1 diversity is provided for comparison. Twenty-five per cent DNA extraction efficiency is assumed for the purposes of this comparison.

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