Microbes (Eukaryotes and Archaea) in sea water from Fildes Peninsula (King George Island, Antarctica)
Citation
Luo W, Li H, Gao S, Yu Y, Lin L, Zeng T, Sweetlove M (2019). Microbes (Eukaryotes and Archaea) in sea water from Fildes Peninsula (King George Island, Antarctica). Version 1.2. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/shi1xi accessed via GBIF.org on 2024-10-04.Description
Amplicon sequencing dataset (Illumina MiSeq) of microbial Eukaryotes (18S ssu rRNA gene), and Archaea in sea water samples taken during the 29th Chinese Antarctic scientific expedition in 2013 at Greatwall cove and Ardley cove, Fildes Peninsula (King George Island, Antarctica).Sampling Description
Study Extent
Samples were taken in January 2013, during the 29th Chinese National Antarctic Research Expedition at Greatwall Cove and Ardley Cove (king George Island, Antarctica)Sampling
1 L of surface sea water from each station was collected and prefiltered through a 20-µm mesh sieve to remove most of the mesozooplankton and large particles, and then directly filtered through a 0.2-µm pore size nucleopore membrane filter (Whatman). The filters were frozen at −80 °C in cetyltrimethylammonium bromide (CTAB) buffer until laboratory experiments were carried out.Method steps
- DNA extraction was performed as described by Luo et al. (2009).
- Polymerase chain reaction (PCR) was performed using primers with barcodes flanking the hypervariable V4 region of the 18S rRNA gene: 3NDf with the reverse primer V4_euk_R2. PCR was conducted in 20 μL reactions with 0.2 μM each of the primers, ~10 ng of template DNA, 1 × PCR buffer, and 2.5 U of Pfu DNA Polymerase (Promega, USA). The amplification programme consisted of an initial denaturation step at 95 °C for 2 min, followed by 30 cycles at 95 °C for 30 s, 55 °C for 30 s, and 72 °C for 30 s, and a final extension of 72 °C for 5 min. PCR products were pooled and purified using a DNA gel extraction kit (Axygen, Hangzhou, China). The DNA concentration of each PCR product was determined using a Quant-iT PicoGreen double-stranded DNA assay (Invitrogen, Germany) and was quality controlled on a TBS-380 Mini-Fluorometer (Turner Biosystems, Sunnyvale, CA, USA). Finally, amplicons of all samples were pooled in equimolar concentrations.
- 18S rRNA amplification and sequencing on the Illumina MiSeq2000 were done by following the standard protocols of Earth Microbiome Project (EMP) (Caporaso et al. 2012).
Taxonomic Coverages
microbial Eukaryotes were sampled based on marker gene amplification (18S ssu rRNA gene)
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Eukaryotacommon name: Eukaryotes rank: domain
Archaea were sampled based on marker gene amplification
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Archaeacommon name: Archaea rank: domain
Geographic Coverages
Fildes Peninsula, King George Island, Antarctica
Bibliographic Citations
- Luo, W., Li, H., Gao, S., Yu, Y., Lin, L., & Zeng, Y. (2016). Molecular diversity of microbial eukaryotes in sea water from Fildes Peninsula, King George Island, Antarctica. Polar Biology, 39(4), 605-616. - https://doi.org/10.1007/s00300-015-1815-8
Contacts
Wei Luooriginator
Polar Research Institute of China
Shanghai
CN
Huirong Li
originator
Polar Research Institute of China
Shanghai
CN
Shengquan Gao
originator
Second Institute of Oceanography
Hangzhou
CN
Yong Yu
originator
Polar Research Institute of China
Shanghai
CN
Ling Lin
originator
Polar Research Institute of China
Shanghai
CN
Tinxin Zeng
originator
Polar Research Institute of China
Shanghai
CN
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
Brussels
1000
email: msweetlove@naturalsciences.be
Wei Luo
administrative point of contact
Polar Research Institute of China
Shanghai
CN