Study of Genetic Diversity of Eukaryotic Picoplankton in Different Oceanic Regions by Small-Subunit rRNA Gene Cloning and Sequencing

Departament de Biologia Marina, Institut de Ciències del Mar, CSIC, E-08039 Barcelona, Catalunya, Spain.
Applied and Environmental Microbiology (Impact Factor: 3.67). 08/2001; 67(7):2932-41. DOI: 10.1128/AEM.67.7.2932-2941.2001
Source: PubMed


Very small eukaryotic organisms (picoeukaryotes) are fundamental components of marine planktonic systems, often accounting for a significant fraction of the biomass and activity in a system. Their identity, however, has remained elusive, since the small cells lack morphological features for identification. We determined the diversity of marine picoeukaryotes by sequencing cloned 18S rRNA genes in five genetic libraries from North Atlantic, Southern Ocean, and Mediterranean Sea surface waters. Picoplankton were obtained by filter size fractionation, a step that excluded most large eukaryotes and recovered most picoeukaryotes. Genetic libraries of eukaryotic ribosomal DNA were screened by restriction fragment length polymorphism analysis, and at least one clone of each operational taxonomic unit (OTU) was partially sequenced. In general, the phylogenetic diversity in each library was rather great, and each library included many different OTUs and members of very distantly related phylogenetic groups. Of 225 eukaryotic clones, 126 were affiliated with algal classes, especially the Prasinophyceae, the Prymnesiophyceae, the Bacillariophyceae, and the Dinophyceae. A minor fraction (27 clones) was affiliated with clearly heterotrophic organisms, such as ciliates, the chrysomonad Paraphysomonas, cercomonads, and fungi. There were two relatively abundant novel lineages, novel stramenopiles (53 clones) and novel alveolates (19 clones). These lineages are very different from any organism that has been isolated, suggesting that there are previously unknown picoeukaryotes. Prasinophytes and novel stramenopile clones were very abundant in all of the libraries analyzed. These findings underscore the importance of attempts to grow the small eukaryotic plankton in pure culture.

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Available from: Carlos Pedrós-Alió, Mar 26, 2014
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    • "For this reason, cultivation-independent molecular surveys have been applied through cloning and sequencing after polymerase chain reaction (PCR), which have demonstrated that protist diversity has been underestimated by orders of magnitude. These findings have thus stimulated renewed interest in protist diversity research within the last decade (Diez et al., 2001;López-Garcia et al., 2001;Moreira and López-Garcia, 2002;Moon-van der Staay et al., 2006). The increase in the numbers of sequences registered in genetic databases for a wide range of microbial eukaryotes offers the possibility to greatly improve the technology used for the study of biodiversity, community structure, and adaptation, and to understand the evolutionary relationships among the many protistan lineages (Caron et al., 2009). "
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    • "Syndiniales Group I was the second main group identified in the present study. Group I belongs to Marine Alveolates Group (MALV) (Díez et al., 2001; López-García et al., 2001; Moon-van der Staay et al., 2001; Groisillier et al., 2006). According to Guillou et al. (2008), Syndiniales Group I are endosymbiont parasites that associate with the Alveolata host cells (Coats & Park, 2002; Guillou et al., 2008). "
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    • "These molecular surveys have been instrumental in decoding the large protist diversity and in unveiling new lineages, such as Picozoa (Not et al., 2007; Seenivasan et al., 2013), marine alveolates (MALV) clades (Guillou et al., 2008) and marine stramenopiles (MAST) clades (Massana et al., 2004; 2014). Earlier molecular surveys were based on clone libraries of near full-length 18S ribosomal (r)DNA genes followed by Sanger sequencing of a subset of the clones (Díez et al., 2001; López-García et al., 2001; Moon-van der Staay et al., 2001). The resulting high-quality, often manually checked environmental sequences have been crucial for the phylogenetic placement of novel clades and, together with sequences from monoclonal cultures, are the basis of reference rDNA databases (Guillou et al., 2013; Pernice et al., 2013). "
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