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Table S1 Primer set used to amplify the D1-D2 region of the Haptophyte LSU rDNA

Table S2 Specificity of our primer set highlighted by in silico analysis.

Table S3 Effect of cleaning.

Table S4 Comparison of community similarities between templates, size fractions and depths as described by anosim values.

Table S5 Number of reads and number of OTU considering LSU1 reads at 99%, 98% and 97% of sequence identity.

Fig. S1 Location of the ‘Mare Chiara’ (MC) station, Bay of Naples, Mediterranean sea.

Fig. S2 Relative position of the LSU1 Haptophyta-specific primer set compared to the LSU rDNA D1-D2 domain.

Fig. S3 Expected D1-D2 LSU rDNA genetic distances at various Haptophyta taxonomic levels.

Fig. S4 Rarefaction analysis of OTU100%, OTU99%, OTU98% and OTU97% pooling reads from the eight samples.

Fig. S5 Taxonomic composition of LSU rDNA reads not assigned to Haptophyta at 85% homology, as inferred from blast analyses in GenBank, using default parameters.

Fig. S6 In the framework of another study, SSU rDNA reads from the V4 and the V9 region were pyrosequenced for the eight same samples from Naples using ‘universal’ eukaryotic primers (details on the primers can be found in Stoeck et al. 2010 or in Logares et al. 2012).

Fig. S7 Boxplots summarizing the range of α-diversity (calculation using Simpson's index) for each condition calculated at 97% clustering level.

Fig. S8 Venn diagrams calculated with OTU97%.

Fig. S9 Heatmap summarizing the % of shared OTU97% between the samples.

Fig. S10 More details on the proportion of reads assigned by phylogenetic mapping for the main Haptophytes lineages.

Fig. S11 Haptophyte community structure based on NMDS (nonmetric multidimensional scaling) ordination of the LSU rDNA dataset distance matrices from OTU97%, followed by comparison of community similarities between depths, size fractions and templates as described by anosim values.

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