In recent years, a substantial amount of data on aquatic protists has been obtained from culture-independent molecular approaches, unveiling a large diversity and the existence of new lineages. However, sequences affiliated with minor groups (in terms of clonal abundance) have often been under-analyzed, and this hides a potentially relevant source of phylogenetic information. Here we have searched public databases for 18S rDNA sequences of chrysophytes, choanoflagellates and bicosoecids retrieved from molecular surveys of protists. These three groups are often considered to account for most of the heterotrophic flagellates, an important functional component in microbial food webs. They represented a significant fraction of clones in freshwater studies, whereas their relative clonal abundance was low in marine studies. The novelty displayed by this dataset was notable. Most environmental sequences were distant to sequences of cultured organisms, indicating a significant bias in the representation of taxa in culture. Moreover, they were often distant to sequences from other molecular surveys, suggesting an insufficient sequencing effort to characterize the in situ diversity of these groups. Phylogenetic trees with complete sequences present the most accurate representation of the diversity of these groups, with the emergence of several new clades formed exclusively by environmental sequences. Exhaustive data mining in sequence databases allowed the identification of new diversity hidden inside chrysophytes, choanoflagellates and bicosoecids.
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