Data from: Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing

• Main Authors: Egge, Elianne Sirnæs, Johannessen, Torill Vik, Andersen, Tom, Eikrem, Wenche, Bittner, Lucie, Larsen, Aud, Sandaa, Ruth-Anne, Edvardsen, Bente, Egge, Elianne Sirnaes
• Format: Dataset
• Language: English
• Published: Dryad 2015
• Subjects: metagenomics; Protists; Microbial Biology; Pavlovophyceae; Prymnesiophyceae; haptophytes; Bioinfomatics/Phyloinfomatics; Haptophyta; Eikrem; Norway; North Atlantic
• Online Access: https://dx.doi.org/10.5061/dryad.b8d21; http://datadryad.org/stash/dataset/doi:10.5061/dryad.b8d21

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. : Environmental data for manuscript mec-14-1145Excel-file containing environmental data from the sampling site OF-2 (59.186668N, 10.691667E), Oslofjorden, Norway, in the study period September 2009-June 2011.Env_data_mec-14-1145.xlsxTable_S2_Egge_et_al_2015_jeukmicTable containing information about the haptophyte V4 SSU rRNA OTUs recorded in Skagerrak in the period September 2009 – June 2011. First published in Egge ES, Eikrem W, Edvardsen B (2015) “Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing”, Journal of Eukaryotic Microbiology 62, 121-140. DOI: 10.1111/jeu.12157Haptophyte_ref_alignment_284taxReference alignment comprising 281 haptophyte 18S rDNA sequences representing all cultured haptophyte species, environmental sequences forming novel clades, and the best BLAST hits in NCBI-nr to the Oslofjorden OTUs. Three outgroup sequences are included (AJ564771 Telonema subtilis, AY919672 Kathablepharis remigera, L28811 Chilomonas paramecium). The sequences from cultured species and environmental sequences that formed novel clades were aligned in MAFFT v.6 with the Q-INS-i strategy (Katoh and Toh 2008). BLAST hits in NCBI-nr that were not already present in the alignment were inserted into the existing alignment using the add-in function in MAFFT for full-length sequences, with method L-INS-1 (Katoh and Frith 2012).MEC-14-1145-OTUtab_piconanopool_notsubsampOTU table, read number not subsampled to even sampling depth.Table of OTU read abundance per sample, subsampled to even sampling depth.OTU table, read number subsampled to even sampling depth (5553 reads).MEC-14-1145-OTUtab_piconanopool_subsamp5553_correctversion.xlsRAxML reference tre of 281 haptophyte taxa + 3 outgroupsMaximum likelihood phylogenetic trees of 281 reference haptophyte sequences (all cultured species + selected environmental sequences) + 3 outgroups (L28811 Chilomonas paramecium, AY919672 Kathablepharis remigera, AJ564771 Telonema subtilis), constructed using RAxML v. 7.3.2 (Stamatakis 2006, Bioinformatics 22:2688-2690), with substitution model GTRCAT and 100 bootstrap runs. RAxML was run on the Lifeportal on the University of Oslo computer cluster (www.lifeportal.uio.no).RAxML_haptophyte_284_taxa_reference_tree.treFasta-file of 156 haptophyte OTUs.Fasta file of 156 haptophyte OTUs, aligned (using MAFFT add-in) to the reference alignment with 281 haptophyte reference sequences.MEC-14-1145-OTUs_aligned.fasta