Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy

@article{GranStadniczeko2017HaptophyteDA,
  title={Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy},
  author={Sandra Gran-Stadnicze{\~n}ko and Luka {\vS}upraha and Elianne Egge and Bente Edvardsen},
  journal={The Journal of Eukaryotic Microbiology},
  year={2017},
  volume={64},
  pages={514 - 532}
}
Haptophyta encompasses more than 300 species of mostly marine pico- and nanoplanktonic flagellates. [] Key Method Samples were collected in August 2013 at the Outer Oslofjorden, Norway. Total RNA/cDNA was amplified by haptophyte-specific primers targeting the V4 region of the 18S, and the D1-D2 region of the 28S rRNA. Taxonomy was assigned using curated haptophyte reference databases and phylogenetic analyses. Both marker genes showed Chrysochromulinaceae and Prymnesiaceae to be the families with highest…
High diversity of haptophytes in the East China Sea revealed by next-generation sequencing and scanning electron microscopy
TLDR
A comparison between the results from NGS and scanning electron microscopy with respect to species diversity and the proportional abundance of coccolithophores showed that NGS had the power to explore overall community diversity, and SEM was capable of a high level of taxonomic resolution to distinguish closely related species with similar 18S rDNA sequences.
Phylogenetic diversity in freshwater‐dwelling Isochrysidales haptophytes with implications for alkenone production
TLDR
Using small‐subunit ribosomal RNA (rRNA) marker gene amplicon high‐throughput sequencing of environmental water column and sediment samples, it is shown that Group I is monophyletic with high phylogenetic diversity and contains a well‐supported clade separating the previously described “EV’ clade from the “Greenland” clade.
Next‐Generation Sequencing to Identify Lacustrine Haptophytes in the Canadian Prairies: Significance for Temperature Proxy Applications
TLDR
It is revealed that most of the LCA-producing OTUs thriving in the Canadian lakes are included within the genus Isochrysis, which helps guide selection of the most appropriate calibration for down-core temperature reconstructions.
The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae
TLDR
The sequenced strain Diacronema lutheri NIVA-4/92, formerly known as Pavlovales, is sequenced because it has established roles in aquaculture and has been a key organism for studying microalgal lipid biosynthesis.
Plankton biodiversity and species co-occurrence based on environmental DNA – a multiple marker study
Metabarcoding in combination with high-throughput sequencing (HTS) allows simultaneous detection of multiple taxa by targeting single or several taxonomically informative gene regions from
Protist Diversity and Seasonal Dynamics in Skagerrak Plankton Communities as Revealed by Metabarcoding and Microscopy
TLDR
This is the first metabarcoding study of the protist plankton community of all taxonomic groups and through seasons in the Skagerrak, which may serve as a baseline for future surveys to reveal effects of climate and environmental changes.
Contrasting Community Composition and Co-Occurrence Relationships of the Active Pico-Sized Haptophytes in the Surface and Subsurface Chlorophyll Maximum Layers of the Arctic Ocean in Summer
Haptophytes (Hacrobia: Haptophyta), which can perform phototrophic, phagotrophic, or mixotrophic nutritional modes, are critical for element cycling in a variety of aquatic ecosystems. However, their
Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment
DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic
The genetic diversity of plastids associated with mixotrophic oligotrich ciliates
TLDR
These results are the first survey of the genetic diversity of plastids associated with pelagic mixotrophic oligotrich ciliates and suggest that some species may selectively retain plastid sequences from certain algal groups, while others appear to be generalists.
...
1
2
3
...

References

SHOWING 1-10 OF 57 REFERENCES
Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing
TLDR
High‐throughput sequencing was used to explore the diversity of haptophytes in outer Oslofjorden, Skagerrak, and supplemented this with electron microscopy to reveal species not yet genetically characterised and some potentially novel taxa.
Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay
TLDR
A large uncharacterized environmental genetic diversity is highlighted, which clearly shows that currently cultivated species poorly reflect the actual diversity present in the natural environment.
Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing
TLDR
Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity, and the seasonal dynamics of OTUs representing putative novel classes (clades HAP‐3–5, or orders) or orders were revealed.
Abundance and diversity of prymnesiophytes in the picoplankton coμmunity from the equatorial Pacific Ocean inferred from 18S rDNA sequences
TLDR
Prymnesiophyte diversity and abundance in natural picoplankton communities is assessed, using a molecular approach, to establish the presence of several prymnesiaophyte lineages with no equivalent among cultivated species.
Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review
TLDR
This work reviews the current knowledge on diversity and distribution of haptophytes revealed by Sanger sequencing of clone libraries and by high-throughput sequencing of amplicons and provides a curated haptophical reference 18S rRNA-gene database for future taxonomic assignment of environmental sequences and metabarcoding reads.
Ribosomal DNA phylogenies and a morphological revision provide the basis for a revised taxonomy of the Prymnesiales (Haptophyta)
TLDR
The rDNA phylogenies indicate that the genus Chrysochromulina is paraphyletic and is divided into two major clades, and suggest a revision of the taxonomy of the Prymnesiales that is in accordance with available molecular evidence and supported by morphological data.
Abundance and diversity of prymnesiophytes in the picoplankton community from the equatorial Pacific Ocean inferred from 18 S rDNA sequences
Picoplankton, i.e., cells smaller than 2–3 mm, dominate in most open oceanic regions, such as in the Pacific Ocean. In these areas, the dominant carotenoid of photosynthetic eukaryotes is
454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes
TLDR
The ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta is tested, and a strategy to more accurately depict haptophyte diversity is proposed.
A taxonomic review of the genus Phaeocystis
TLDR
The picture emerging from both molecular and morphological data is that the number of species in the genus is still underestimated and that cryptic or pseudocryptic diversity requires a sound assessment in future research of this genus.
Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing.
TLDR
This extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.
...
1
2
3
4
5
...