Figure S1. Depth profiles of temperature from the Mediterranean Sea station H01 (top graph) in January 2006 (closed triangles) and in May 2003 (open circles); and from the Sragasso Sea BATS114 station (bottom graph) in March 1998 (closed triangles) and July 1998 (open circles).

Figure S2.GC plots ofPRs from the Mediterranean and SargassoSeas. GC plots of environmental PR DNA sequences were visualized using the GCviz script (Zeidner et al., 2005) written in the R-language ( Fifty random sequences from each station, season and depth were aligned on top of each other and a sliding window of 30 nt with a 5 nt step was used. Color code index indicates %GC. White boxes represent windows with missing nucleotide data and black colored pixels represent %GC values lower than 20. Plots are separated according to station, season and depth as in Fig. 3.

Figure S3. Estimated likelihood of samples being drawn from the same population. Red cells indicate that two samples arise from indistinguishable parent populations. Dark pink cells indicate that one sample appears to be a subsample of the other, without a reciprocal relationship. Light pink indicates borderline probabilities of sharing a common population. Blue cells indicate a 0.0000 = p estimate for the probability of being drawn from the same population. The Jan and March samples are ‘mixed’ stations, which correlates well with their lack of structure.

Figure S4. Logarithmic transmission of downwelling irradiance for different wavelengths in the Sargasso and Mediterranean Seas. Sargasso Sea (black line) and the Mediterranean Sea (gray line). Based on calculating attenuation coefficients, Kd (). For the Mediterranean Sea Kd (443) = 0.0348 m-1, Kd (555)= 0.0760 m-1, Kd (665) = 0.3991 m-1, For the Sargasso Sea Kd (441) 0.0398 m-1, Kd (555) = 0.0741 m-1, Kd (665) = 0.4382 m-1.

Figure S5. Relationship between Mediterranean Sea and Sargasso Sea GPR and BPR proteins retrieved from different depths and seasons. A Neighbour-joining phylogenetic tree of Mediterranean PR protein sequences amplified from 0, 20 and 55 m and Sargasso PRs from 0, 40 and 80 m from mixed and stratified samples. Names of the PR sequences were removed for clarity. Environmental sequences are represented by black (BPRs) or white (GPRs) bands corresponding to their predicted absorption maxima to illustrate their distribution in different depths and seasons. The two subfamilies previously reported to be spectrally tuned (Béjà et al., 2001) are marked in black and white boxes. SAR86 and SAR11 PR families, as well as few different PR representative’s names from the Pacific Ocean (Béjà et al., 2001), Sargasso Sea shotgun-sequencing project (Venter et al., 2004), Mediterranean Sea BACs (Sabehi et al., 2003; Sabehi et al., 2004; Sabehi et al., 2005), Pelagibacter ubique(Giovannoni et al., 2005) and marine Archaea(Frigaard et al., 2006) are indicated to serve as orientation marks. Different groups discussed in the text are marked with grey boxes while groups in which spectral tuning is suggested are marked with an empty box. Pyrocystis lunula (Okamoto and Hastings, 2003) was used to root the tree and is not shown.

Figure S6.GPRs and BPRsdepth distribution in the Mediterranean and SargassoSeas. Pie charts represent percentages ofGPRs (marked in white) and BPRs (marked in black) at different depths in the stations sampled. Data extracted from the Sargasso Sea shotgun-sequencing project (Venter et al., 2004) is presented on the right. The percentages presented in the different pies are [GPRs %, BPRs %, n= number of clones], [61, 39, n=147], [44, 56, n=169], [9, 91, n= 75] and [36, 64, n= 90], [31, 69, n= 103], [41, 59, n=103] in the 0, 20 and 55 m samples of the stratified and mixed Mediterranean station, respectively. In the Sargasso Sea station, only BPRs were detected except for the stratified 40 m sample, which contained 0.01% GPRs (1 out of total 414 sequences). In the data from the Sargasso Sea metagenome, 2% GPRs were detected [n=291].

References

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