Widespread distribution of a unique marine protistan lineage

Cuvelier, Marie L.; Ortiz, Alejandra; Kim, Eun-Soo; Moehlig, Heike; Richardson, David E.; Heidelberg, John F.; Archibald, John M.; Worden, Alexandra Z.

doi:10.1111/j.1462-2920.2008.01580.x

Cited by 55 publications

(76 citation statements)

References 45 publications

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“…The size of these organisms has been the subject of recent discussion, with related sequences obtained from cells in the nanoplankton size range (2-20 mm). These larger 'biliphytes' were found in greater abundance (28% of all protist clones) in tropical eddy-influenced surface waters (Cuvelier et al, 2008). Our single-cell sequencing-based analysis indicates that biliphytes comprised a significant fraction of small protists in the studied sample from the Gulf of Maine.…”

Section: Discussionmentioning

confidence: 81%

Capturing diversity of marine heterotrophic protists: one cell at a time

et al. 2010

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Recent applications of culture-independent, molecular methods have revealed unexpectedly high diversity in a variety of functional and phylogenetic groups of microorganisms in the ocean. However, none of the existing research tools are free from significant limitations, such as PCR and cloning biases, low phylogenetic resolution and others. Here, we employed novel, single-cell sequencing techniques to assess the composition of small (o10 lm diameter), heterotrophic protists from the Gulf of Maine. Single cells were isolated by flow cytometry, their genomes amplified, and 18S rRNA marker genes were amplified and sequenced. We compared the results to traditional environmental PCR cloning of sorted cells. The diversity of heterotrophic protists was significantly higher in the library of single amplified genomes (SAGs) than in environmental PCR clone libraries of the 18S rRNA gene, obtained from the same coastal sample. Libraries of SAGs, but not clones contained several recently discovered, uncultured groups, including picobiliphytes and novel marine stramenopiles. Clone, but not SAG, libraries contained several large clusters of identical and nearly identical sequences of Dinophyceae, Cercozoa and Stramenopiles. Similar results were obtained using two alternative primer sets, suggesting that PCR biases may not be the only explanation for the observed patterns. Instead, differences in the number of 18S rRNA gene copies among the various protist taxa probably had a significant role in determining the PCR clone composition. These results show that single-cell sequencing has the potential to more accurately assess protistan community composition than previously established methods. In addition, the creation of SAG libraries opens opportunities for the analysis of multiple genes or entire genomes of the uncultured protist groups.

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Section: Discussionmentioning

confidence: 81%

Capturing diversity of marine heterotrophic protists: one cell at a time

et al. 2010

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“…Our previous study showed that picobiliphytes are prevalent in eutrophic waters (Cheung et al, 2008), and this finding is supported by the results obtained in this study (Figure 1). The repeated recovery of picobiliphytes in our samples also provides further evidence on their prevalence in subtropical waters (Cheung et al, 2008, Cuvelier et al, 2008. NAGIII, a newly defined alveolates group, contains environmental sequences from oceanic and coastal waters .…”

Section: Diversity Of the Picoeukaryotic Assemblagesmentioning

confidence: 84%

Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing

et al. 2010

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Information on genetic diversity of picoeukaryotes (o2-3 lm) comes mainly from traditional gene cloning and sequencing, but this method suffers from cloning biases and limited throughput. In this study, we explored the feasibility of using the cloning-independent and massively parallel 454 pyrosequencing technology to study the composition and genetic diversity of picoeukaryotes in the coastal waters of the subtropical western Pacific using the hypervariable V4 region of the 18S rRNA gene. Picoeukaryote assemblages between two sites with different hydrography and trophic status were also compared. The approach gave a high coverage of the community at genetic difference X5% but still underestimated the total diversity at a genetic difference p2%. Diversity of picoeukaryotes was higher in an oligomesotrophic bay than in a eutrophic bay. Stramenopiles, dinoflagellates, ciliates and prasinophytes were the dominant groups comprising approximately 27, 19, 11 and 11%, respectively, of the picoeukaryotes. Water samples collected from the two bays contained different high-level taxonomic groups and phylotype operational taxonomic units of picoeukaryotes. Our study represents one of the first and most comprehensive examinations of marine picoeukaryotic diversity using the 454 sequencing-by-synthesis technology.

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“…The paucity of cultured picophytoeukaryotes from this and other divisions is a major restriction on physiological and ecological research on photosynthetic picoeukaryotes. We also know there are lineages for which there is not a single cultured representative (e.g., Not et al 2007b;Cuvelier et al 2008), these will be discussed in later sections.…”

Section: Photoautotrophsmentioning

confidence: 99%