Résumé
Haptophytes are a key phylum of marine protists, including ~300 described
morphospecies and 80 morphogenera. We used 454 pyrosequencing on large
subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from
size-fractioned plankton samples collected in the Bay of Naples. One
group-specific primer set targeting the LSU rDNA D1/D2 region was designed
to amplify Haptophyte sequences from nucleic acid extracts (total DNA or
RNA) of two size fractions (0.8–3 or 3–20 μm) and two sampling depths
[subsurface, at 1 m, or deep chlorophyll maximum (DCM) at 23 m]. 454 reads
were identified using a database covering the entire Haptophyta diversity
currently sequenced. Our data set revealed several hundreds of Haptophyte
clusters. However, most of these clusters could not be linked to
taxonomically known sequences: considering OTUs97% (clusters build at a
sequence identity level of 97%) on our global data set, less than 1% of
the reads clustered with sequences from cultures, and less than 12%
clustered with reference sequences obtained previously from cloning and
Sanger sequencing of environmental samples. Thus, we highlighted a large
uncharacterized environmental genetic diversity, which clearly shows that
currently cultivated species poorly reflect the actual diversity present
in the natural environment. Haptophyte community appeared to be
significantly structured according to the depth. The highest diversity and
evenness were obtained in samples from the DCM, and samples from the large
size fraction (3–20 μm) taken at the DCM shared a lower proportion of
common OTUs97% with the other samples. Reads from the species Chrysoculter
romboideus were notably found at the DCM, while they could be detected at
the subsurface. The highest proportion of totally unknown OTUs97% was
collected at the DCM in the smallest size fraction (0.8–3 μm). Overall,
this study emphasized several technical and theoretical barriers inherent
to the exploration of the large and largely unknown diversity of
unicellular eukaryotes.