title: Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean.
abstract: BACKGROUND
  Photosynthetic picoeukaryotes (PPE) with a cell size less than 3 microm play a critical role in oceanic primary production. In recent years, the composition of marine picoeukaryote communities has been intensively investigated by molecular approaches, but their photosynthetic fraction remains poorly characterized. This is largely because the classical approach that relies on constructing 18S rRNA gene clone libraries from filtered seawater samples using universal eukaryotic primers is heavily biased toward heterotrophs, especially alveolates and stramenopiles, despite the fact that autotrophic cells in general outnumber heterotrophic ones in the euphotic zone.
  
  
  RESULTS
  In order to better assess the composition of the eukaryotic picophytoplankton in the South East Pacific Ocean, encompassing the most oligotrophic oceanic regions on earth, we used a novel approach based on flow cytometry sorting followed by construction of 18S rRNA gene clone libraries. This strategy dramatically increased the recovery of sequences from putative autotrophic groups. The composition of the PPE community appeared highly variable both vertically down the water column and horizontally across the South East Pacific Ocean. In the central gyre, uncultivated lineages dominated: a recently discovered clade of Prasinophyceae (IX), clades of marine Chrysophyceae and Haptophyta, the latter division containing a potentially new class besides Prymnesiophyceae and Pavlophyceae. In contrast, on the edge of the gyre and in the coastal Chilean upwelling, groups with cultivated representatives (Prasinophyceae clade VII and Mamiellales) dominated.
  
  
  CONCLUSIONS
  Our data demonstrate that a very large fraction of the eukaryotic picophytoplankton still escapes cultivation. The use of flow cytometry sorting should prove very useful to better characterize specific plankton populations by molecular approaches such as gene cloning or metagenomics, and also to obtain into culture strains representative of these novel groups.
authors.affiliation: UPMC (Paris-06) and CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France.
authors.forename: Xiao Li
authors.initials: XL
authors.lastname: Shi
authors.forename: Dominique
authors.initials: D
authors.lastname: Marie
authors.forename: Ludwig
authors.initials: L
authors.lastname: Jardillier
authors.forename: David J
authors.initials: DJ
authors.lastname: Scanlan
authors.forename: Daniel
authors.initials: D
authors.lastname: Vaulot
mesh_terms: D003001:Cloning, Molecular; D019295:Computational Biology / Q000379:methods; D005057:Eukaryotic Cells / Q000145:classification; D005434:Flow Cytometry / Q000379:methods; D015723:Gene Library; D020459:Genes, rRNA; D010140:Pacific Ocean; D010788:Photosynthesis; D010802:Phylogeny; D010933:Plankton / Q000145:classification* / Q000235:genetics*; D016133:Polymerase Chain Reaction; D012337:RNA, Ribosomal, 18S / Q000737:chemistry; D012623:Seawater; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D012337:RNA, Ribosomal, 18S