Bacteria in Antarctic glacial foreland soils
Citation
Yan W, Ma H, Shi G, Sun B, Xiao X, Zhang Y, Sweetlove M (2019). Bacteria in Antarctic glacial foreland soils. Version 1.3. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/6pzeer accessed via GBIF.org on 2024-08-19.Description
Amplicon sequencing dataset (Illumina MiSeq) of Bacteria (16S ssu rRNA) in an Antarctic glacial foreland soil gradientSampling Description
Study Extent
Soil samples were collected from the glacial foreland in Larsemann Hills in East Antarctica (-69.39762S, 76.40666 E), during the 29th Chinese National Antarctic Research Expedition in the Antarctic summer in February 2013.Sampling
Surface soil layers, approximately 5 cm, were collected. When sites were covered by ice (3,4 and 5), the covering ice was gently cracked and the ice fractures were removed before sampling the soil beneath. The samples were stored in plastic bags and kept at -20°C during transport and storage in the laboratory until they were used for further analysis.Method steps
- Each soil sample was homogenized and sub-sampled for DNA extraction and geochemical measurements.
- An SDS-based method was employed to extract the DNA from soil (Natarajan et al., 2016). The bacterial V4 region of the 16S rRNA gene was amplified with a special bacterial primer pair 533F (TGCCAGCAGCCGCGGTAA)/Bact806R (GGACTACCAGGGTATCTAATCCTGTT). A sample tagging approach was employed, and a different barcode was added before the forward primer for each sample. The PCR reagents were mixed as follow: 5 μl of 10× Taq buffer (Takara, Otsu, Shiga, Japan), 4 μl of dNTP (Takara, Otsu, Shiga, Japan), 1 μl of each primer (10 μM stored concentration), 0.25 μl of Ex Taq DNA polymerase (Takara, Otsu, Shiga, Japan), approximately 50 ng of DNA, 2.5 μl of BSA (Bull Serum Albumin), and 32.75 μl of water. The PCR amplification consisted of an initial denaturation at 94°C for 5 min; 25 cycles of denaturation at 94°C for 40 s, annealing at 58°C for 40 s, and extension at 72°C for 1 min; and a final extension at 72°C for 8 min. The PCR products were purified with a Gel Extraction Kit (Omega Bio-Tek, Norcross, GA, United States) according to the manufacturer’s instructions.
- The reads were obtained with MiSeq sequencing platform (Illumina, San Diego, CA, United States).
Taxonomic Coverages
Bacteria 16S ssu rRNA marker gene, v4 region
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Bacteriacommon name: Bacteria rank: domain
Geographic Coverages
Soil samples were collected from the glacial foreland in Larsemann Hills in East Antarctica
Bibliographic Citations
- Yan, W., Ma, H., Shi, G., Li, Y., Sun, B., Xiao, X., & Zhang, Y. (2017). Independent Shifts of Abundant and Rare Bacterial Populations across East Antarctica Glacial Foreland. Frontiers in microbiology, 8, 1534. -
Contacts
Wenkai Yanoriginator
Shanghai Jiao Tong University
Shanghai
CN
Hongmei Ma
originator
Polar Research Institute of China
Shanghai
CN
Guitao Shi
originator
Polar Research Institute of China
Shanghai
CN
Bo Sun
originator
Polar Research Institute of China
Shanghai
CN
Xiang Xiao
originator
Shanghai Jiao Tong University
Shanghai
CN
Yu Zhang
originator
Shanghai Jiao Tong University
Shanghai
CN
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
Brussels
1000
BE
email: msweetlove@naturalsciences.be
Wenkai Yan
administrative point of contact
Shanghai Jiao Tong University
Shanghai
CN