Bacteria in Antarctic glacial foreland soils

Versão mais recente published by SCAR - Microbial Antarctic Resource System on mar 19, 2019 SCAR - Microbial Antarctic Resource System
Publication date:
19 de março de 2019
Licença:
CC-BY 4.0

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Descrição

Amplicon sequencing dataset (Illumina MiSeq) of Bacteria (16S ssu rRNA) in an Antarctic glacial foreland soil gradient

Versões

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Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

Yan W, Ma H, Shi G, Sun B, Xiao X, Zhang Y (2018): Bacteria in Antarctic glacial foreland soils. v1.3. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacteria_antarctic_glacial_foreland_soils&v=1.3

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: 8e7cf0b8-4789-4b79-9dc9-33d65ed79918.  SCAR - Microbial Antarctic Resource System publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por Scientific Committee on Antarctic Research.

Palavras-chave

Metadata

Contatos

Wenkai Yan
  • Originador
  • Ponto De Contato
Shanghai Jiao Tong University
Shanghai
CN
Hongmei Ma
  • Originador
Polar Research Institute of China
Shanghai
CN
Guitao Shi
  • Originador
Polar Research Institute of China
Shanghai
CN
Bo Sun
  • Originador
Polar Research Institute of China
Shanghai
CN
Xiang Xiao
  • Originador
Shanghai Jiao Tong University
Shanghai
CN
Yu Zhang
  • Originador
Shanghai Jiao Tong University
Shanghai
CN
Maxime Sweetlove
  • Provedor Dos Metadados
Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
1000 Brussels
BE

Cobertura Geográfica

Soil samples were collected from the glacial foreland in Larsemann Hills in East Antarctica

Coordenadas delimitadoras Sul Oeste [-69, 76,407], Norte Leste [-69, 76,407]

Cobertura Taxonômica

Bacteria 16S ssu rRNA marker gene, v4 region

Domínio Bacteria (Bacteria)

Dados Sobre o Projeto

Nenhuma descrição disponível

Título Bacteria in Antarctic glacial foreland soils
Financiamento Funding was provided by the National Natural Science Foundation of China (grants 41276202, 41476123, 41676177), China Ocean Mineral Resources R&D Association (grants DY125-22-04), and the thirteen Five-Year Plan for Polar Science (grants CHINARE 2016-02-02).

O pessoal envolvido no projeto:

Wenkai Yan

Métodos de Amostragem

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.

Área de Estudo 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.

Descrição dos passos do método:

  1. Each soil sample was homogenized and sub-sampled for DNA extraction and geochemical measurements.
  2. 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.
  3. The reads were obtained with MiSeq sequencing platform (Illumina, San Diego, CA, United States).

Citações bibliográficas

  1. 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.

Metadados Adicionais

Identificadores alternativos 8e7cf0b8-4789-4b79-9dc9-33d65ed79918
https://ipt.biodiversity.aq/resource?r=bacteria_antarctic_glacial_foreland_soils