Fig. S1. Relative cyanophage abundance at the RW, Narragansett Bay site from 2005 to 2010. Estimates are based on the most probable number assay using Synechococcus sp. WH7803 as a host.

Fig. S2. Rarefaction curves for the four data sets used in this study (RW time series, SNE, Bermuda and Environmental Clones).

Fig. S3. Monthly relative abundance of two common OTUs (RIM2 and RIM50) at the RW, Narragansett Bay site. Blue, RIM50; red, RIM2; small black squares, data not available (see Table S2 for sampling dates).

Fig. S4. (A) Rarified number of OTUs and (B) rarified Shannon Diversity for the SNE, Long Island NY and Bermuda sites.

Fig. S5. Non-metric multidimensional scaling plot of samples from nine SNE sites samples based on pair-wise Bray-Curtis similarity values calculated using the relative abundance of OTUs in each sample. Samples are coloured by season.

Fig. S6. Map of the four Bermuda sites used to isolate cyanophages via the extinction-dilution method. 2, Castle Harbour; 5, Harrington Sound; 8, Mills Creek; 9, Long Island.

Table S1. Number and per cent of clones (n = 318) belonging to OTUs that also include cyanophage isolates. OTUs in bold belong to the 10 most abundant OTUs based on 1726 SNE isolates. RW is located in Narragansett Bay and Sn is located in Cape Cod Bay.

Table S2. Number of myoviral isolates characterized (number of OTUs) for each sampling site and date. Only isolates obtained via the extinction-dilution method are included in the table. Missing values indicate that cyanophage isolation was not attempted in these months.

Table S3. Coordinates of sampling locations and ranges of temperature and salinity at each site.

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