scholarly journals An 18S V4 rDNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000 m depth

2021 ◽  
Author(s):  
Elianne Egge ◽  
Stephanie Elferink ◽  
Daniel Vaulot ◽  
Uwe John ◽  
Gunnar Bratbak ◽  
...  
Keyword(s):  
Arctic Ocean ◽  
High Throughput Sequencing ◽  
Sea Water ◽  
Size Fraction ◽  
The Arctic ◽  
Reference Database ◽  
Rrna Gene ◽  
Svalbard Archipelago ◽  
The Arctic Ocean ◽  
Epipelagic Zone

AbstractArctic marine protist communities have been understudied due to challenging sampling conditions, in particular during winter and in deep waters. The aim of this study was to improve our knowledge on Arctic protist diversity through the year, both in the epipelagic (< 200 m depth) and mesopelagic zones (200-1000 m depth). Sampling campaigns were performed in 2014, during five different months, to capture the various phases of the Arctic primary production: January (winter), March (pre-bloom), May (spring bloom), August (post-bloom) and November (early winter). The cruises were undertaken west and north of the Svalbard archipelago, where warmer Atlantic waters from the West Spitsbergen Current meets cold Arctic waters from the Arctic Ocean. From each cruise, station, and depth, 50 L of sea water were collected and the plankton was size-fractionated by serial filtration into four size fractions between 0.45-200 µm, representing the picoplankton, nanoplankton and microplankton. In addition vertical net hauls were taken from 50 m depth to the surface at selected stations. From the plankton samples DNA was extracted, the V4 region of the 18S rRNA-gene was amplified by PCR with universal eukaryote primers and the amplicons were sequenced by Illumina high-throughput sequencing. Sequences were clustered into Amplicon Sequence Variants (ASVs), representing protist genotypes, with the dada2 pipeline. Taxonomic classification was made against the curated Protist Ribosomal Reference database (PR2). Altogether 6,536 protist ASVs were obtained (including 54 fungal ASVs). Both ASV richness and taxonomic composition were strongly dependent on size-fraction, season, and depth. ASV richness was generally higher in the smaller fractions, and higher in winter and the mesopelagic samples than in samples from the well-lit epipelagic zone during summer. During spring and summer, the phytoplankton groups diatoms, chlorophytes and haptophytes dominated in the epipelagic zone. Parasitic and heterotrophic groups such as Syndiniales and certain dinoflagel-lates dominated in the mesopelagic zone all year, as well as in the epipelagic zone during the winter. The dataset is available at https://doi.org/10.17882/79823, (Egge et al., 2014).

scholarly journals An 18S V4 rDNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000 m depth

2021 ◽  
Author(s):  
Elianne Egge ◽  
Stephanie Elferink ◽  
Daniel Vaulot ◽  
Uwe John ◽  
Gunnar Bratbak ◽  
...  
Keyword(s):  
Arctic Ocean ◽  
High Throughput Sequencing ◽  
Sea Water ◽  
Size Fraction ◽  
The Arctic ◽  
Reference Database ◽  
Rrna Gene ◽  
Svalbard Archipelago ◽  
The Arctic Ocean ◽  
Epipelagic Zone

Abstract. Arctic marine protist communities have been understudied due to challenging sampling conditions, in particular during winter and in deep waters. The aim of this study was to improve our knowledge on Arctic protist diversity through the year, both in the epipelagic (< 200 m depth) and mesopelagic zones (200–1000 m depth). Sampling campaigns were performed in 2014, during five different months, to capture the various phases of the Arctic primary production: January (winter), March (pre-bloom), May (spring bloom), August (post-bloom) and November (early winter). The cruises were undertaken west and north of the Svalbard archipelago, where warmer Atlantic waters from the West Spitsbergen Current meets cold Arctic waters from the Arctic Ocean. From each cruise, station, and depth, 50 L of sea water were collected and the plankton was size-fractionated by serial filtration into four size fractions between 0.45–200 μm, representing the picoplankton, nanoplankton and microplankton. In addition vertical net hauls were taken from 50 m depth to the surface at selected stations. From the plankton samples DNA was extracted, the V4 region of the 18S rRNA-gene was amplified by PCR with universal eukaryote primers and the amplicons were sequenced by Illumina high-throughput sequencing. Sequences were clustered into Amplicon Sequence Variants (ASVs), representing protist genotypes, with the dada2 pipeline. Taxonomic classification was made against the curated Protist Ribosomal Reference database (PR2). Altogether 6,536 protist ASVs were obtained (including 54 fungal ASVs). Both ASV richness and taxonomic composition were strongly dependent on size-fraction, season, and depth. ASV richness was generally higher in the smaller fractions, and higher in winter and the mesopelagic samples than in samples from the well-lit epipelagic zone during summer. During spring and summer, the phytoplankton groups diatoms, chlorophytes and haptophytes dominated in the epipelagic zone. Parasitic and heterotrophic groups such as Syndiniales and certain dinoflagellates dominated in the mesopelagic zone all year, as well as in the epipelagic zone during the winter. The dataset is available at https://doi.org/10.17882/79823 (Egge et al. 2014).

scholarly journals An 18S V4 rRNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000 m depth

2021 ◽  
Vol 13 (10) ◽  
pp. 4913-4928
Author(s):  
Elianne Egge ◽  
Stephanie Elferink ◽  
Daniel Vaulot ◽  
Uwe John ◽  
Gunnar Bratbak ◽  
...  
Keyword(s):  
Arctic Ocean ◽  
High Throughput Sequencing ◽  
18S Rrna Gene ◽  
The Arctic ◽  
Reference Database ◽  
Rrna Gene ◽  
Svalbard Archipelago ◽  
Size Fractions ◽  
The Arctic Ocean ◽  
Epipelagic Zone

Abstract. Arctic marine protist communities have been understudied due to challenging sampling conditions, in particular during winter and in deep waters. The aim of this study was to improve our knowledge on Arctic protist diversity through the year, in both the epipelagic (< 200 m depth) and mesopelagic zones (200–1000 m depth). Sampling campaigns were performed in 2014, during five different months, to capture the various phases of the Arctic primary production: January (winter), March (pre-bloom), May (spring bloom), August (post-bloom), and November (early winter). The cruises were undertaken west and north of the Svalbard archipelago, where warmer Atlantic waters from the West Spitsbergen Current meet cold Arctic waters from the Arctic Ocean. From each cruise, station, and depth, 50 L of seawater was collected, and the plankton was size-fractionated by serial filtration into four size fractions between 0.45–200 µm, representing picoplankton (0.45–3 µm), small and large nanoplankton (3–10 and 10–50 µm, respectively), and microplankton (50–200 µm). In addition, vertical net hauls were taken from 50 m depth to the surface at selected stations. The net hauls were fractionated into the large nanoplankton (10–50 µm) and microplankton (50–200 µm) fractions. From the plankton samples DNA was extracted, the V4 region of the 18S rRNA-gene was amplified by polymerase chain reaction (PCR) with universal eukaryote primers, and the amplicons were sequenced by Illumina high-throughput sequencing. Sequences were clustered into amplicon sequence variants (ASVs), representing protist genotypes, with the dada2 pipeline. Taxonomic classification was made against the curated Protist Ribosomal Reference database (PR2). Altogether, 6536 protist ASVs were obtained (including 54 fungal ASVs). Both ASV richness and taxonomic composition varied between size fractions, seasons, and depths. ASV richness was generally higher in the smaller fractions and higher in winter and the mesopelagic samples than in samples from the well-lit epipelagic zone during summer. During spring and summer, the phytoplankton groups diatoms, chlorophytes, and haptophytes dominated in terms of relative read abundance in the epipelagic zone. Parasitic and heterotrophic groups such as Syndiniales and certain dinoflagellates dominated in the mesopelagic zone all year, as well as in the epipelagic zone during the winter. The dataset is available at https://doi.org/10.17882/79823 (Egge et al., 2014).

scholarly journals Distribution of PAHs and the PAH-degrading bacteria in the deep-sea sediments of the high-latitude Arctic Ocean

2014 ◽  
Vol 11 (9) ◽  
pp. 13985-14021 ◽  
Author(s):  
C. Dong ◽  
X. Bai ◽  
H. Sheng ◽  
L. Jiao ◽  
H. Zhou ◽  
...  
Keyword(s):  
Arctic Ocean ◽  
Deep Sea ◽  
High Throughput Sequencing ◽  
The Arctic ◽  
Rrna Gene ◽  
Long Distance ◽  
Degrading Bacteria ◽  
The Arctic Ocean ◽  
Deep Sea Sediments

Abstract. Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants, which can be transferred to a long distance and tend to accumulation in marine sediment. However, PAHs distribution and natural bioattenuation is less known in open sea, especially in the Arctic Ocean. In this report, sediment samples were collected at four sites from the Chukchi Plateau to Makarov Basin in the summer of 2010. PAH composition and total concentrations were examined with GC-MS, we found that the concentrations of 16 EPA-priority PAHs varied from 2.0 to 41.6 ng g−1 dry weight in total and decreased with sediment depths and as well as from the southern to northern sites. Among the targeted PAHs, phenanthrene was relatively abundant in all sediments. To learn the diversity of bacteria involved in PAHs degradation in situ, the 16S rRNA gene of the total environmental DNA was analyzed with Illumina high throughput sequencing (IHTS). In all the sediments, occurred the potential degraders including Cycloclasticus, Pseudomonas, Halomonas, Pseudoalteromonas, Marinomonas, Bacillus, Dietzia, Colwellia, Acinetobacter, Alcanivorax, Salinisphaera and Shewanella, with Dietzia as the most abundant. Meanwhile on board, enrichment with PAHs was initiated and repeated transfer in laboratory to obtain the degrading consortia. Most above mentioned bacteria in addition to Hahella, Oleispira, Oceanobacter and Hyphomonas, occurred alternately as a predominant member in enrichment cultures from different sediments, as revealed with IHTS and PCR-DGGE. To reconfirm their role in PAH degradation, 40 different bacteria were isolated and characterized, among which Cycloclasticus and Pseudomonas showed the best degradation capability under low temperature. Taken together, PAHs and PAH-degrading bacteria were widespread in the deep-sea sediments of the Arctic Ocean. We propose that bacteria of Cycloclasticus, Pseudomonas, Pseudoalteromonas, Halomonas, Marinomonas and Dietzia may play the most important role in PAHs mineralization in situ.

scholarly journals Relationship Between Carbon- and Oxygen-Based Primary Productivity in the Arctic Ocean, Svalbard Archipelago

2019 ◽  
Vol 6 ◽  
Author(s):  
Marina Sanz-Martín ◽  
María Vernet ◽  
Mattias R. Cape ◽  
Elena Mesa ◽  
Antonio Delgado-Huertas ◽  
...  
Keyword(s):  
Arctic Ocean ◽  
Primary Productivity ◽  
The Arctic ◽  
Svalbard Archipelago ◽  
The Arctic Ocean

scholarly journals Pliocene cooling enhanced by flow of low-salinity Bering Sea water to the Arctic Ocean

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Keiji Horikawa ◽  
Ellen E. Martin ◽  
Chandranath Basak ◽  
Jonaotaro Onodera ◽  
Osamu Seki ◽  
...  
Keyword(s):  
Arctic Ocean ◽  
Bering Sea ◽  
Sea Water ◽  
The Arctic ◽  
Low Salinity ◽  
The Arctic Ocean

scholarly journals Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean

2015 ◽  
Vol 81 (6) ◽  
pp. 2137-2148 ◽  
Author(s):  
Mary Thaler ◽  
Connie Lovejoy
Keyword(s):  
Arctic Ocean ◽  
Water Column ◽  
High Throughput Sequencing ◽  
Species Level ◽  
The Arctic ◽  
Heterotrophic Flagellate ◽  
Sequencing Data ◽  
Content Type ◽  
The Arctic Ocean ◽  
Taxonomic Groups

ABSTRACTHeterotrophic marine flagellates (HF) are ubiquitous in the world's oceans and represented in nearly all branches of the domain Eukaryota. However, the factors determining distributions of major taxonomic groups are poorly known. The Arctic Ocean is a good model environment for examining the distribution of functionally similar but phylogenetically diverse HF because the physical oceanography and annual ice cycles result in distinct environments that could select for microbial communities or favor specific taxa. We reanalyzed new and previously published high-throughput sequencing data from multiple studies in the Arctic Ocean to identify broad patterns in the distribution of individual taxa. HF accounted for fewer than 2% to over one-half of the reads from the water column and for up to 60% of reads from ice, which was dominated byCryothecomonas. In the water column, many HF phylotypes belonging to Telonemia and Picozoa, uncultured marine stramenopiles (MAST), and choanoflagellates were geographically widely distributed. However, for two groups in particular, Telonemia andCryothecomonas, some species level taxa showed more restricted distributions. For example, several phylotypes of Telonemia favored open waters with lower nutrients such as the Canada Basin and offshore of the Mackenzie Shelf. In summary, we found that while some Arctic HF were successful over a range of conditions, others could be specialists that occur under particular conditions. We conclude that tracking species level diversity in HF not only is feasible but also provides a potential tool for understanding the responses of marine microbial ecosystems to rapidly changing ice regimes.

The Contribution of Bering Sea Water to the Arctic Ocean

ARCTIC ◽  
1961 ◽  
Vol 14 (3) ◽  
Author(s):  
L.K. Coachman ◽  
C.A. Barnes
Keyword(s):  
Arctic Ocean ◽  
Bering Sea ◽  
Sea Water ◽  
The Arctic ◽  
The Arctic Ocean

scholarly journals Diversity and Distribution of Marine Microbial Eukaryotes in the Arctic Ocean and Adjacent Seas

2006 ◽  
Vol 72 (5) ◽  
pp. 3085-3095 ◽  
Author(s):  
C. Lovejoy ◽  
R. Massana ◽  
C. Pedr�s-Ali�
Keyword(s):  
Arctic Ocean ◽  
18S Rrna Gene ◽  
Ocean Basin ◽  
Significant Loss ◽  
Canada Basin ◽  
The Arctic ◽  
Rrna Gene ◽  
The North ◽  
The Arctic Ocean ◽  
Upper Mixed Layer

ABSTRACT We analyzed microbial eukaryote diversity in perennially cold arctic marine waters by using 18S rRNA gene clone libraries. Samples were collected during concurrent oceanographic missions to opposite sides of the Arctic Ocean Basin and encompassed five distinct water masses. Two deep water Arctic Ocean sites and the convergence of the Greenland, Norwegian, and Barents Seas were sampled from 28 August to 2 September 2002. An additional sample was obtained from the Beaufort Sea (Canada) in early October 2002. The ribotypes were diverse, with different communities among sites and between the upper mixed layer and just below the halocline. Eukaryotes from the remote Canada Basin contained new phylotypes belonging to the radiolarian orders Acantharea, Polycystinea, and Taxopodida. A novel group within the photosynthetic stramenopiles was also identified. One sample closest to the interior of the Canada Basin yielded only four major taxa, and all but two of the sequences recovered belonged to the polar diatom Fragilariopsis and a radiolarian. Overall, 42% of the sequences were <98% similar to any sequences in GenBank. Moreover, 15% of these were <95% similar to previously recovered sequences, which is indicative of endemic or undersampled taxa in the North Polar environment. The cold, stable Arctic Ocean is a threatened environment, and climate change could result in significant loss of global microbial biodiversity.

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