Citation:

PANGAEA.963976

Name: Species determination in plankton net (20 µm) concentrates by DNA sequencing during the PHYCOB cruise in the Southwestern Black Sea in 2021
Published: 2024-01-09
License: https://creativecommons.org/licenses/by/4.0/
Keywords: chlorophyll-a; CTD profile; HAB species; isolated strains; net tows; NOC; Nutrient data; phycotoxins; POC; vitamin B12

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Published: 2024-01-09 • DOI registered: 2024-02-07

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Abstract:

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.

Keyword(s):

chlorophyll-a; CTD profile; HAB species; isolated strains; net tows; NOC; Nutrient data; phycotoxins; POC; vitamin B12

References:

Dzhembekova, Nina; Urusizaki, Shingo; Moncheva, Snejana; Ivanova, Petya; Nagai, Satoshi (2017): Applicability of massively parallel sequencing on monitoring harmful algae at Varna Bay in the Black Sea. Harmful Algae, 68, 40-51, https://doi.org/10.1016/j.hal.2017.07.004

Schoch, Conrad L; Ciufo, Stacy; Domrachev, Mikhail; Hotton, Carol L; Kannan, Sivakumar; Khovanskaya, Rogneda; Leipe, Detlef; Mcveigh, Richard; O'Neill, Kathleen; Robbertse, Barbara; Sharma, Shobha; Soussov, Vladimir; Sullivan, J P; Sun, Lu; Turner, Seán; Karsch-Mizrachi, Ilene (2020): NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database, baaa062, https://doi.org/10.1093/database/baaa062

Tanabe, Akifumi S; Nagai, Satoshi; Hida, Kohsuke; Yasuike, Motoshige; Fujiwara, Atushi; Nakamura, Yoji; Takano, Yoshihito; Katakura, Seiji (2016): Comparative study of the validity of three regions of the 18S- rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community. Molecular Ecology Resources, 16(2), 402-414, https://doi.org/10.1111/1755-0998.12459

Coverage:

Median Latitude: 43.321191 * Median Longitude: 29.429765 * South-bound Latitude: 42.233500 * West-bound Longitude: 28.124900 * North-bound Latitude: 44.582100 * East-bound Longitude: 31.047683

Date/Time Start: 2021-09-12T04:20:00 * Date/Time End: 2021-09-17T10:00:00

Minimum Elevation: -2154.0 m * Maximum Elevation: -33.0 m

Event(s):

PHYCOB_1 * Latitude: 42.913300 * Longitude: 30.371802 * Date/Time: 2021-09-12T04:20:00 * Elevation: -1946.0 m * Campaign: * Basis: * Method/Device: Multiple investigations (MULT)

PHYCOB_2 * Latitude: 43.152700 * Longitude: 30.718115 * Date/Time: 2021-09-12T08:20:00 * Elevation: -1935.0 m * Campaign: * Basis: * Method/Device: Multiple investigations (MULT)

PHYCOB_3 * Latitude: 43.383200 * Longitude: 31.047683 * Date/Time: 2021-09-12T11:30:00 * Elevation: -1398.0 m * Campaign: * Basis: * Method/Device: Multiple investigations (MULT)

Comment:

Data provider:

Nataliya Slabakova

Nina Dzhembekova

Snejana Moncheva

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Event label	Event
2	Latitude of event	Latitude
3	Longitude of event	Longitude
4	Date/Time of event	Date/Time
5	Code	Code		Dzhembekova, Nina		InstitutionCode
6	Code	Code		Dzhembekova, Nina		CollectionCode
7	Provenance/source	Source		Dzhembekova, Nina
8	Species	Species		Dzhembekova, Nina	Basic Local Alignment Search Tool (BLAST)	of the reference sequence/sequences with the highest percent identity after BLAST search
9	Genetic lineage	Gen lineage		Dzhembekova, Nina	According to Schoch et al. (2020)
10	Identity	Ident	%	Dzhembekova, Nina	Basic Local Alignment Search Tool (BLAST)	according to BLAST results
11	Location	Location		Dzhembekova, Nina
12	Country	Country		Dzhembekova, Nina
13	Depth, top/min	Depth top	m	Dzhembekova, Nina
14	Depth, bottom/max	Depth bot	m	Dzhembekova, Nina
15	Reads	Reads	#	Dzhembekova, Nina	Basic Local Alignment Search Tool (BLAST)	Number of sequence reads

License:

Creative Commons Attribution 4.0 International (CC-BY-4.0)

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

8272 data points

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