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Figs S1–S5. Phylogenetic trees illustrating the relationship of SSU rRNA gene sequences from genomes and uncultivated clones represented on the genome-proxy microarray (blue) and their close relatives (black) as ‘landmarks’. Support for dendrogram topologies is indicated by bootstrap values at nodes determined by the maximum likelihood method (only values > 50 are shown). The outgroups used were Methanomethylovorans victoriae strain TM (AJ276437) for the bacterial dendrograms, and Myxococcus xanthus strain UCDaV1 (AY724797) for the archaeal dendrogram. *The publicly available SSU rDNA sequence for the Roseobacter-like alphaproteobacterial clone HTCC2255 (AATR01000062) is from a Gammaproteobacterium, known to have contaminated the HTCC2255 culture (http://www.roseobase.org/roseo/htcc2255.html). S1.Gamma- and Betaproteobacteria. S2.Alphaproteobacteria. S3.Deltaproteobacteria and Spirochaetes. S4. Other Bacteria. S5.Archaea.

Fig. S2. Alphaproteobacterial array targets (blue) and their close ‘landmark’ relatives (black).

Fig. S3. Deltaproteobacterial and Spirochaete array targets (blue) and their close ‘landmark’ relatives (black).

Fig. S4. Other bacterial array targets (blue) and their close ‘landmark’ relatives (black).

Fig. S5. Archaeal array targets (blue) and their close ‘landmark’ relatives (black).

Fig. S6. Origin of array targets and their relative array-based occurrences in Monterey Bay and Hawaii samples. A. Derivation of array targets, either as environmental genome fragments from Hawaii (blue), Monterey (green), other marine sites (beige), or from marine microbial genomes (black). The number of targets in each category is indicated. B. The proportional abundance of each target type in 57 Monterey Bay samples, measured as the relative proportion of total array signal across all samples hybridized.

Fig. S7. Mixed layer depth (MLD) over the sampling period, with hybridized samples indicated. MLD was calculated as the first depth (≥ 10 m) with > 0.1°C difference from the previous meter (per MBARI BOG group, R. Michisaki, pers. comm.). X-axis indicates sampling date in continuous numbered days since 1 January 2000, and y-axis indicates depth. Dashed red line highlights 30 m depth. Trendline shows moving average of MLD with period of 2. The MLD at this location is typically deepest in the winters and shallowest towards the end of the spring/summer upwelling season. Samples of 30 m were both within and below the ML, and the site shows high MLD variability.

Fig. S8. Clustering of hybridizations by sample and by genotype, per Fig. 4, using only the subset of the 30 m samples definitively below the mixed layer depth (MLD). MLD is shown in Fig. S7 and was calculated as the first depth (≥ 10 m) with > 0.1°C difference from the previous meter (per MBARI BOG group, R. Michisaki, pers. comm.). Excluding the 30 m samples above the MLD does not result in discrete clustering of the 0 m and 30 m samples.

Fig. S9. Array profiles for all targets within three common phylogenetic clades: (A) Roseobacter, (B) SAR86, (C) SAR11.

Fig. S10. Heatmap of array hybridizations with samples ordered chronologically, without clustering of samples (columns) or genotypes (rows). The break between the 2000–2002 and 2003–2004 sampling periods is indicated by the black vertical dashed line. Intensity of cell colour indicates relative target signal for that genotype and sample date; note that relative abundance is quantitative for each genotype between samples but not between genotypes. Samples are named Depth_Year_CollectionDate, and are colour-coded by oceanographic season (see colour legend and text). Red asterisks denote samples with particularly intense 0 m profiles. Grey columns indicate no samples for that depth and date. (A) 0 m samples, (B) 30 m samples, (C) 200 m samples, with the three depths vertically stacked.

Fig. S11. Evaluating the genetic relatedness of community DNA hybridized to the array. On the left are mean organism signals as shown in Fig. 4, repeated here for side-by-side examination. On the right are the relative ratios of the Tukey biweights (TBW) to the means for each organism (samples in same order as clustering based on mean signals, on left). This ratio is related to the identity of hybridized DNA to the target sequence. Hybridized DNAs with a large relative drop in signal when assessed as TBW rather than as mean (darker blue) have a less even signal across their target probe sets, and are thus inferred to be less closely related to the target sequence (i.e. 80–90% ANI), whereas hybridized DNAs with higher TBW:Mean ratios (lighter blue) are inferred to be genotypes more closely related to targeted sequences (i.e. > 90% ANI), as in Rich and colleagues (2008).

Table S1. Array targets

Table S2. Array targets summarized by phylogenetic cluster

Table S3. Comparison of array with other broad taxonomic surveys of Monterey Bay.

Table S4. Nutrient data for the sample site (Station M1) 2000–2004.

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