Amplicon sequencing dataset (454 LS) targeting planktonic Bacteria (16S ssu rRNA) in surface layer sea water samples (n=18) from the Northern tip of the Antarctic Peninsula.
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Cao S, He J, Zhang F, Lin L, Gao Y, Zhou Q (2021): Bacterioplankton in surface waters off the northern tip of the Antarctic Peninsula. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacterioplankton_from_northern_tip_antarctic_peninsula&v=1.0
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Northern tip of the Antarctic Peninsula
|Bounding Coordinates||South West [-65.613, -66.441], North East [-64.815, -62.593]|
|Start Date / End Date||2011-12-30 / 2012-01-29|
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|Funding||This work was funded by the Chinese Polar Environment Comprehensive Investigation & Assessment Programs (CHINARE-2011–2015), an international cooperation programme of the Chinese National Arctic and Antarctic Research Expedition (IC201514) and the National Natural Science Foundation of China (grant nos. 41206189 and 41476168).|
|Study Area Description||Seawater from the northern tip of the Antarctic Peninsula.|
The personnel involved in the project:
Thirteen samples were taken at 25 m depth (the layer of maximum oxygen), three samples were taken at 2 m and two samples were taken at 50 m depth. An SBE 911 plus CTD instrument combined with an SBE 32 Carousel water sampler (both by Sea-Bird Electronics) equipped with 24 Niskin bottles was used to collect seawater and measure physical parameters (temperature and salinity). +- 2 L of seawater was pre-filtered through 3 μm pore size polycarbonate membranes (Whatman), and then filtered with a vacuum pump through polycarbonate membranes (47 mm diameter, 0.2-μm pore size, Whatman). Samples were subsequently frozen at −80°C.
|Study Extent||Samples (n=18) were collected in the waters by the northern tip of the Antarctic Peninsula, including the northern area of the Bransfield Strait, the Powell Basin and the South Orkney tableland area during the 28th Chinese National Antarctic Research Expedition, from December 2011 to January 2012.|
|Quality Control||The PCR products were purified using AxyPrepTM DNA Purification Kit (Axygen®) and quantified using a Qubit® 2.0 Fluorometer (Life Technologies).|
Method step description:
- DNA was extracted using a modified cetyltrimethylammonium bromide method and examined by agarose gel electrophoresis.
- The V1–V3 region of the 16S rRNA gene of Bacteria was amplified using the universal primer pair F8 (5′-CCTATCCCCTGTGT- GCCTTGGCAGTCTCAG-AGAGTTTGATCCTGGCTCAG-3′) and R533 (5′-CCATCTCATCCCTGC- GTGTCTCCGACTCAG-NNNNNNNN-TTACCGCGGCTGCT- GGCAC-3′; NNNNNNNN being the place of the sample-specific barcode). PCR was performed using 5–10 ng genomic DNA in a final volume of 50 μL. The PCR procedure was as follows: initial denaturation at 95°C for 2 min; 25 cycles at 95°C for 30 s, 56.4°C for 1 min and 72°C for 30 s; and a final extension at 72°C for 5 min.
- 454 pyrosequencing was performed on an FLX Titanium Genome Sequencer (454/Roche Life Sciences).
- Cao, S., He, J., Zhang, F., Lin, L., Gao, Y., & Zhou, Q. (2019). Diversity and community structure of bacterioplankton in surface waters off the northern tip of the Antarctic Peninsula. Polar Research.