Groups without Cultured Representatives Dominate Eukaryotic Picophytoplankton in the Oligotrophic South East Pacific Ocean

Abstract

BackgroundPhotosynthetic picoeukaryotes (PPE) with a cell size less than 3 µm 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.Methodology/Principal FindingsIn 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/SignificanceOur 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.

Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean

“…Moreover, plastid 16S rRNA gene sequences of photosynthetic chrysophytes have recently been reported from various marine environments (Fuller et al, 2006a, b;McDonald et al, 2007;Lepère et al, 2009) highlighting the potentially wide distribution and ecological importance of this class. Furthermore, 18S rRNA gene sequences of marine chrysophytes forming new groups without cultured representatives and comprising putative photosynthetic organisms have also been retrieved in several recent studies (Worden and Not, 2008;Shi et al, 2009).…”

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

“…Node support is shown for (black circles) 100% and (black triangles) ≥75% support. Uncultured prymnesiophytes have also been seen recently in the South Pacific (40).…”

A global perspective on marine photosynthetic picoeukaryote community structure

“…However, relative hybridisation values rarely exceeded 10% (Figure 3). Their low abundance in open ocean waters has also been observed using fluorescent in situ hybridisation analysis (for example, 1-3% of phototrophic cells in the Indian Ocean and o1% in the northern North Atlantic (Kirkham et al, 2011b)) and by 18S and 16S rRNA gene sequencing Lepère et al, 2009;Shi et al, 2009;Kirkham et al, 2011a). This class appears to be mostly restricted to coastal waters (see, for example, Romari and Vaulot, 2004).…”