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Fig. S1. Maximum likelihood phylogenetic tree of 18S rDNA haptophyte sequences showing all prymnesiophyte OTUs retrieved in this study, their first hit by blast against the SILVA database SSU104 and sequences representing known orders and environmental lineages, including partially overlapping sequences to our sequences, especially including sequences retrieved from freshwaters. Two cryptophyte sequences were used as outgroup. The alignment contained 1682 selected positions. Positions on a 2147 bp alignment having less than 50% gaps were retained to reconstruct the tree using BMGE. 18S rRNA gene sequences from this work are shown in bold. Full circles indicate sequences of freshwater and salty continental habitats; other sequences are from marine ecosystems. Bootstrap values greater than 50% are shown at nodes (1000 replicates). The scale bar represents the number of substitutions per 100 positions per a unit branch length.

Fig. S2. Maximum likelihood phylogenetic tree of 18S rDNA haptophyte sequences of marine, freshwater and salty continental habitats. This tree was built using the same sequences as in Fig. 3 plus shorter and/or partially overlapping environmental sequences related to our sequences. The 82 prymnesiophyte sequences used to construct the tree are shown collapsed. The alignment contained 1678 selected positions (positions with less than 50% gaps were selected using BMGE on a 2131 bp alignment). 18S rRNA gene sequences from this work are shown in bold. Full circles indicate freshwater sequences; other sequences are from marine ecosystems. Bootstrap values greater than 50% are shown at nodes (1000 replicates). The scale bar represents the number of substitutions per 100 positions per unit branch length.

Table S1. Major characteristics of the samples analysed in this study. The positive or negative amplification of 18S rRNA genes with prymnesiophyte (Prym.) or pavlovophyte (Pav.)- specific primers is indicated with ‘+’ or ‘−’ signs. n.a., not applicable; n.d., not done.

Table S2. OTUs identified in this work. The name of representative sequences for each OTU, their first BLAST hit in the Silva Database SSU104, their percentage of similarity as well as the total number of sequences retrieved in each system are given.

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