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Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean

By Xiao Li Shi, D. Marie, Ludwig Jardillier, David J. Scanlan and Daniel Vaulot

Abstract

Background: Photosynthetic 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. \ud Methodology/Principal Findings: 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. \ud Conclusions/Significance: 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

Topics: QK, QH426
Publisher: Public Library of Science
Year: 2009
OAI identifier: oai:wrap.warwick.ac.uk:2715

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  1. (1988). A novel free-living prochlorophyte occurs at high cell concentrations in the oceanic euphotic zone. doi
  2. (2004). A single species Micromonas pusilla (Prasinophyceae) dominates the eukaryotic picoplankton in the western English Channel. doi
  3. (2000). Abundance and diversity of prymnesiophytes in the picoplankton community from the equatorial Pacific Ocean inferred from 18S rDNA sequences. doi
  4. (2006). Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids. doi
  5. (1999). Bolidomonas: a new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta). doi
  6. (2006). Clusterer: extendable java application for sequence grouping and cluster analyses.
  7. (2004). Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. doi
  8. (2007). Contribution of picoplankton to the total particulate organic carbon concentration in the eastern South Pacific. doi
  9. (2008). Control of toxic marine dinoflagellate blooms by serial parasitic killers. doi
  10. (2002). Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. doi
  11. (2009). Defining DNA-based Operational Taxonomic Units for microbial-eukaryote ecology. doi
  12. (2008). Distribution of micro-organisms along a transect in the South-East Pacific Ocean (BIOSOPE cruise) from epifluorescence microscopy. doi
  13. (2004). Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems. doi
  14. (2008). Ecological niche partitioning in the picoplanktonic green alga Micromonas pusilla: evidence from environmental surveys using phylogenetic probes. doi
  15. (2006). Eukaryotic picoplankton communities of the Mediterranean Sea in summer assessed by molecular approaches (DGGE, TTGE, doi
  16. (2008). Fe ´rre ´ol M, Vaulot D
  17. (2008). Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II. doi
  18. (2009). Grazing rates and functional diversity of uncultured heterotrophic flagellates. doi
  19. (2009). Haptophyta rule the waves: Extreme oceanic biodiversity in non-calcifying haptophytes explains the 19-Hex paradox.
  20. (2008). High bacterivory by the smallest phytoplankton in the North Atlantic Ocean. doi
  21. (2008). Introduction to the special section biooptical and biogeochemical conditions in the South East Pacific in late 2004: the BIOSOPE program. doi
  22. (2002). Macroecological patterns of phytoplankton in the northwestern North Atlantic Ocean. doi
  23. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. doi
  24. (2005). Microplankton assemblages at Station KNOT in the subarctic western Pacific, doi
  25. (1998). Modeltest: testing the model of DNA substitution. doi
  26. (2006). Molecular analysis of photosynthetic picoeukaryote community structure along an Arabian Sea transect. doi
  27. (2002). Novel kingdom-level eukaryotic diversity in anoxic environments. doi
  28. (2001). Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. doi
  29. (2003). Parmales (Chrysophyceae) from the Gulf of Tehuantepec, Mexico, including the description of a new species, Tetraparma insecta sp Nov., and a proposal to the taxonomy of the group. doi
  30. (1987). Parmales, a new order of marine chrysophytes, with descriptions of three new genera and seven new species. doi
  31. (2002). PAUP*. Phylogenetic analysis using parsimony (*and others methods). 4 ed. doi
  32. (2006). Pedros Alio C doi
  33. (2006). Phylogenetic affinities of an enigmatic nannoplankton, Braarudosphaera bigelowii based on the SSU rDNA sequences. doi
  34. (2004). Phylogenetic and ecological analysis of novel marine stramenopiles. doi
  35. (2007). Picobiliphytes, a new marine picoplanktonic algal group with unknown affinities to other eukaryotes. doi
  36. (2008). Picoplankton diversity in the South-East Pacific Ocean from cultures. doi
  37. (1994). Primary production of prochlorophytes, cyanobacteria, and eucaryotic ultraphytoplankton: measurements from flow cytometric sorting. doi
  38. r eC ,V a u l o tD ,S c a n l a nD
  39. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. doi
  40. (2008). Spatial variability of phytoplankton pigment distributions in the Subtropical South Pacific Ocean: comparison between in situ and predicted data. doi
  41. (1987). Structural diversity of eukaryotic small subunit ribosomal RNAs. Evolutionary implications. doi
  42. (2001). Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. doi
  43. (2008). The diversity of small eukaryotic phytoplankton (#3 mm) in marine ecosystems. doi
  44. (2001). Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton.
  45. Vaulot D (submitted) Diversity of small photosynthetic eukaryotes in the English Channel from samples sorted by flow cytometry. doi
  46. (2008). Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). doi
  47. (1979). Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium. doi
  48. (2007). Zingone A doi

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