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  • 1
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    The ocean sampling day consortium (2015)
    Oxford Univ. Press
    In:  GigaScience, 4 (1). Art.Nr. 27.
    Details
    Publication Date: 2019-09-23
    Description: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
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    DOI: 10.1186/s13742-015-0066-5
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 2
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    Data collection of the PHYCOB cruise with focus on harmfula algal species in the Southwestern Black Sea in 2021 (2024)
    PANGAEA
    Details
    Publication Date: 2024-02-07
    Description: The data set was acquired during the PHYCOB cruise in the frame of the Eurofleets+ programme (https://www.eurofleets.eu/2021/10/22/phycob-an-international-oceanographic-expedition-into-the-western-black-sea-coordinated-by-the-alfred-wegner-institut-helmholtz-zentrum-fur-polar-und-meeresforschung-awi/) within the Regional call in the territorrial waters of Romania and Bulgaria in the Western Baltic Sea from 11th to 17th September 2021. The aim of the cruise was to assess the occurrence of potentially harmfal algae and their associated phycotoxins in the Black Sea and the accompanying environmental parameters. Sampling was performed by CTD casts and Rosette water sampling in addition to vertical phytoplankton net hauls from 30 m depth to surface. The determined parameters include the following: Quantitative phytoplankton cell counts in water samples, qulitative determination of toxigenic species next generation sequencing data in plankton net concentrates, monoclonanal cultures established from water sample isolates, phycotoxins in plankton net concentrates, inorganic nitruinets (nitrate/nitrite, phosphate, silicate) , vitamin B12, particulate organic carbon, particulate organic nitrogen, flowcytometry data, and CTD data (temperature, salinity, chlorophyll-a, oxygen, turbidity, radiance).
    Keywords: chlorophyll-a; CTD profile; HAB species; isolated strains; net tows; NOC; Nutrient data; phycotoxins; POC; vitamin B12
    Type: Dataset
    Format: application/zip, 8 datasets
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 3
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    Species determination in plankton net (20 µm) concentrates by light microscopy during the PHYCOB cruise in the Southwestern Black Sea in 2021 (2024)
    PANGAEA
    Details
    Publication Date: 2024-02-07
    Description: At each station two vertical net tows were taken from the water column using a 20 μm plankton net (438-030, Hydro-Bios, Kiel, Germany) for analyses of plankton and phycotoxins. The depth of the hauls was fixed to 0 - 30 m. The collected net tow concentrates were adjusted to 1 L with filtered seawater. 50 mL aliquots were fixed with formaldehyde solution, buffered to pH 8-8.2 with disodiumtetraborate (4% final concentration) for microscopic analyses of phytoplankton. Taxonomic identification and cell counts of the net samples were done under inverted microscope (Nikon Eclipse TE2000-U) connected to a video-interactive image analysis system (L.U.C.I.A, Version 4.8, Laboratory Imaging Ltd, Prague, Czech Republic) at 400 × magnification in Sedgwick-Rafter counting chambers. Only dinoflagellates species and the diatom Pseudo-nitzschia genus were considered during the analyses. 400 cells were counted from each sample, while rare and large species were checked in the whole counting chamber (Moncheva and Parr 2010). Cell abundance was expressed in cells per net tow. Taxonomic nomenclature was according to the on-line data-base of World Register of Marine Species (WoRMS) http://www.marinespecies.org/. The QC/QA of the data was performed following the quality control Guidelines for phytoplankton (Moncheva 2010). IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae was used as a reference database of toxic microalgal species selection.
    Keywords: chlorophyll-a; Class; Code; Comment; Country; Counts; CTD profile; Date; Depth, bottom/max; Depth, top/min; Event label; Family; Genus; HAB species; Investigator; isolated strains; Kingdom; LATITUDE; Location; LONGITUDE; MULT; Multiple investigations; net tows; NOC; Nutrient data; Order; PHYCOB; PHYCOB_1; PHYCOB_10; PHYCOB_11; PHYCOB_12; PHYCOB_13; PHYCOB_14; PHYCOB_15; PHYCOB_16; PHYCOB_17; PHYCOB_18; PHYCOB_19; PHYCOB_2; PHYCOB_20; PHYCOB_21; PHYCOB_22; PHYCOB_23; PHYCOB_3; PHYCOB_4; PHYCOB_5; PHYCOB_6; PHYCOB_7; PHYCOB_8; PHYCOB_9; phycotoxins; Phylum; POC; Provenance/source; Sample ID; Scientific name; Species; Species, unique identification (Semantic URI); Species, unique identification (URI); Tübitak Marmara; vitamin B12; Year of analysis
    Type: Dataset
    Format: text/tab-separated-values, 22397 data points
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    DATA PANGAEA
  • 4
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    Species determination in plankton net (20 µm) concentrates by DNA sequencing during the PHYCOB cruise in the Southwestern Black Sea in 2021 (2024)
    PANGAEA
    Details
    Publication Date: 2024-02-07
    Description: At each station two vertical net tows were taken from the water column using a 20 μm plankton net (438-030, Hydro-Bios, Kiel, Germany) for analyses of plankton and phycotoxins. The depth of the hauls was fixed to 0 – 30 m. The collected net tow concentrates were adjusted to 1 L with filtered seawater. 150 mL aliquots were filtered under gentle vacuum (〈 0.2 bar) through 1 μm pore-size polycarbonate filters (Whatman, USA) for DNA analysis. DNA from the filters was immediately extracted by using 5% Chelex buffer (Tanabe et al. 2016). For detection of eukaryotic species, universal primers for 18S rRNA gene V7-V9 variable region (18S-V7F: TGGAGYGATHTGTCTGGTTDATTCCG and 18S-V9R: TCACCTACGGAWACCTTGTTACG; modified from Tanabe et al. 2016) were used. The procedures and techniques, applicable to the treatment of the obtained sequences, selection and taxonomic identification of operational taxonomic units (OTUs), were administered according to the workflow described in Dzhembekova et al. (2017). Taxonomic assignment was performed using BLAST against a sequence database downloaded from GenBank.
    Keywords: According to Schoch et al. (2020); Basic Local Alignment Search Tool; BLAST; chlorophyll-a; Code; Country; CTD profile; Date/Time of event; Depth, bottom/max; Depth, top/min; Event label; Genetic lineage; HAB species; Identity; isolated strains; Latitude of event; Location; Longitude of event; MULT; Multiple investigations; net tows; NOC; Nutrient data; PHYCOB; PHYCOB_1; PHYCOB_10; PHYCOB_11; PHYCOB_12; PHYCOB_13; PHYCOB_14; PHYCOB_15; PHYCOB_16; PHYCOB_17; PHYCOB_18; PHYCOB_19; PHYCOB_2; PHYCOB_20; PHYCOB_21; PHYCOB_22; PHYCOB_23; PHYCOB_3; PHYCOB_4; PHYCOB_5; PHYCOB_6; PHYCOB_7; PHYCOB_8; PHYCOB_9; phycotoxins; POC; Provenance/source; Reads; Species; Tübitak Marmara; vitamin B12
    Type: Dataset
    Format: text/tab-separated-values, 8272 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 5
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    New Knowledge on Distribution and Abundance of Toxic Microalgal Species and Related Toxins in the Northwestern Black Sea (2022)
    MDPI
    In:  EPIC3Toxins, MDPI, 14(10), pp. 685, ISSN: 2072-6651
    Details
    Publication Date: 2022-10-16
    Description: Numerous potentially toxic plankton species commonly occur in the Black Sea, and phycotoxins have been reported. However, the taxonomy, phycotoxin profiles, and distribution of harmful microalgae in the basin are still understudied. An integrated microscopic (light microscopy) and molecular (18S rRNA gene metabarcoding and qPCR) approach complemented with toxin analysis was applied at 41 stations in the northwestern part of the Black Sea for better taxonomic coverage and toxin profiling in natural populations. The combined dataset included 20 potentially toxic species, some of which (Dinophysis acuminata, Dinophysis acuta, Gonyaulax spinifera, and Karlodinium veneficum) were detected in over 95% of the stations. In parallel, pectenotoxins (PTX-2 as a major toxin) were registered in all samples, and yessotoxins were present at most of the sampling points. PTX-1 and PTX-13, as well as some YTX variants, were recorded for the first time in the basin. A positive correlation was found between the cell abundance of Dinophysis acuta and pectenotoxins, and between Lingulodinium polyedra and Protoceratium reticulatum and yessotoxins. Toxic microalgae and toxin variant abundance and spatial distribution was associated with environmental parameters. Despite the low levels of the identified phycotoxins and their low oral toxicity, chronic toxic exposure could represent an ecosystem and human health hazard.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
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    PAPER (OA)
  • 6
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    The ocean sampling day consortium (2015)
    BioMed Central
    Details
    Publication Date: 2022-10-18
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5.
    Description: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Description: This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.
    Keywords: Ocean sampling day ; OSD ; Biodiversity ; Genomics ; Health index ; Bacteria ; Microorganism ; Metagenomics ; Marine ; Micro B3 ; Standards
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Limitation Availability
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    PAPER (OA)
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