Deep‐branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing

Egge, Elianne; Eikrem, Wenche; Edvardsen, Bente

doi:10.1111/jeu.12157

Cited by 51 publications

(80 citation statements)

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“…This demonstrates how high throughput sequencing of amplicon libraries is a powerful tool for detecting haptophyte species not yet morphologically and genetically characterized [48,49]. The level of haptophyte richness measured in Raunefjorden (93 different haptophyte OTUs) was at the same order of magnitude as the level previously found in Oslofjorden (156 haptophyte OTUs), a study for which the same sequencing technology and primers were used [47]. The loss of reads in the filtering process (Table S3) was high but can be explained by the fact that the multiplex identification tag was only present on the forward primer, leading to loss of nearly half of the reads.…”

Section: Discussionmentioning

confidence: 72%

Seasonal Dynamics of Haptophytes and dsDNA Algal Viruses Suggest Complex Virus-Host Relationship

Johannessen

Larsen

Bratbak

et al. 2017

Viruses

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Viruses influence the ecology and diversity of phytoplankton in the ocean. Most studies of phytoplankton host–virus interactions have focused on bloom-forming species like Emiliania huxleyi or Phaeocystis spp. The role of viruses infecting phytoplankton that do not form conspicuous blooms have received less attention. Here we explore the dynamics of phytoplankton and algal viruses over several sequential seasons, with a focus on the ubiquitous and diverse phytoplankton division Haptophyta, and their double-stranded DNA viruses, potentially with the capacity to infect the haptophytes. Viral and phytoplankton abundance and diversity showed recurrent seasonal changes, mainly explained by hydrographic conditions. By 454 tag-sequencing we revealed 93 unique haptophyte operational taxonomic units (OTUs), with seasonal changes in abundance. Sixty-one unique viral OTUs, representing Megaviridae and Phycodnaviridae, showed only distant relationship with currently isolated algal viruses. Haptophyte and virus community composition and diversity varied substantially throughout the year, but in an uncoordinated manner. A minority of the viral OTUs were highly abundant at specific time-points, indicating a boom-bust relationship with their host. Most of the viral OTUs were very persistent, which may represent viruses that coexist with their hosts, or able to exploit several host species.

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Section: Discussionmentioning

confidence: 72%

Seasonal Dynamics of Haptophytes and dsDNA Algal Viruses Suggest Complex Virus-Host Relationship

Johannessen

Larsen

Bratbak

et al. 2017

Viruses

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“…RNA extraction, PCR, Roche/454 pyrosequencing, processing of the reads and phylogenetic analyses are described in detail in Egge et al . (2015). Briefly, each date, 20 L sea water from 1 m depth was size-fractionated to 0.8–3 and 3–45 μm by in-line peristaltic filtration onto polycarbonate filters.…”

Section: Methodsmentioning

confidence: 99%

“…Rigorous cleaning of the reads was performed as described in Egge et al . (2015). Briefly, it included the following steps, with number of remaining OTUs assigned to Haptophyta after each step given in parentheses: denoising with ampliconnoise v. 1.26 (Quince et al .…”

Section: Methodsmentioning

confidence: 99%

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Seasonal diversity and dynamics of haptophytes in theSkagerrak,Norway, explored by high‐throughput sequencing

et al. 2015

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Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2 years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September–October (autumn) and lowest in April–May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3–5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters.

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“…For the 28 Haptophyta OTUs, we first downloaded 106 GenBank accessions following a previously described taxon-sampling method 22,72,73 , and aligned them in MAFFT 74 v7. OTU representatives were then added to this alignment using the MAFFT 'add-in' function, and the tree was inferred with RAxML, using the substitution model GTR-G-I, the new rapid hill-climbing algorithm and 100 bootstrap runs.…”

Section: Stampa Plotsmentioning

confidence: 99%

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

et al. 2017

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High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.S ince the works of early naturalists such as von Humboldt and Bonpland 1 , we have known that animal and plant communities in tropical rainforests are exceedingly species rich. For example, one hectare can contain more than 400 tree species 2 and one tree can harbour more than 40 ant species 3 . This hyperdiversity of trees has been partially explained by the Janzen-Connell model 4,5 , which hypothesizes that host-specific predators and parasites reduce plant population growth in a density-dependent manner 6,7 . Sampling up in the tree canopies and below on the ground has further led to the view that arthropods are the most diverse eukaryotes in tropical rainforests 8,9 .The focus on eukaryotic macroorganisms in these studies is primarily because they are familiar and readily observable to us. We do not know whether the less familiar and less readily observable protists-microbial eukaryotes that are not animals, plants or fungi 10 -inhabiting these same ecosystems exhibit similar diversity patterns. To evaluate if macroorganismic diversity patterns are reflected at the microbial scale with protists, we conducted an environmental DNA metabarcoding study by sampling soils in 279 locations in a variety of lowland Neotropical forest types in La Selva Biological Station, Costa Rica, Barro Colorado Island, Panama and Tiputini Biodiversity Station, Ecuador. This metabarcoding approach has the power to uncover known and new taxa on a massive scale 11 . By amplifying DNA extracted from the soils with broadly targeted primers for the V4 region of 18S rRNA and sequencing it using the Illumina MiSeq platform, we were able to detect most eukaryotic lineages, and assess the diversity and relative dominance of free-living and parasitic lineages.

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Deep‐branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing

Cited by 51 publications

References 84 publications

Seasonal Dynamics of Haptophytes and dsDNA Algal Viruses Suggest Complex Virus-Host Relationship

Seasonal Dynamics of Haptophytes and dsDNA Algal Viruses Suggest Complex Virus-Host Relationship

Seasonal diversity and dynamics of haptophytes in theSkagerrak,Norway, explored by high‐throughput sequencing

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

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