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Microbiome (Archaea, Bacteria and Fungi) in soils from King George Island (Antarctica)

Dernière version Publié par SCAR - Microbial Antarctic Resource System le 19 mars 2019 SCAR - Microbial Antarctic Resource System
Amplicon sequencing dataset (Illumina MiSeq) of Bacteria (16S); Archaea (16S) and Fungi (ITS) in soils from the Fildes region on King George Island (Antarctica).
Date de publication:
19 mars 2019
Licence:
CC-BY 4.0

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Zhang Y, Lu L, Chang X, Jiang F, Gao X, Yao Y, Cao S, Zhou Q, Peng F (2019): Microbiome (Archaea, Bacteria and Fungi) in soils from King George Island (Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbiome_soil_king_george_island_antarctica&v=1.1

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L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

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Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 0e3185d2-7264-4487-b77a-b559de2f2a79.  SCAR - Microbial Antarctic Resource System publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Scientific Committee on Antarctic Research.

Mots-clé

Metadata

Contacts

Personne ayant créé cette ressource:

Yumin Zhang
Wuhan University
Wuhan
CN
Lu Lu
Wuhan University
Wuhan
CN
Xulu Chang
Wuhan University
Wuhan
CN
Fan Jiang
Wuhan University
Wuhan
CN
Xiangdong Gao
Wuhan University
Wuhan
CN
Yifeng Yao
Chinese Academy of Sciences
Beijing
CN
Shunan Cao
Polar Research Institute of China
Shanhai
CN
Qiming Zhou
ChosenMed Technology (Beijing) Company Limited
Beijing
CN
Fang Peng
Wuhan University
Wuhan
CN

Personne pouvant répondre aux questions sur la ressource:

Yumin Zhang
Wuhan University
Wuhan
CN

Personne ayant renseigné les métadonnées:

Maxime Sweetlove
Research assistent
Royal Belgian Institute of Natural Sciences
Rue vautier 29
1000 Brussels
BE

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

Fildes region on the King George island, Antarctica

Enveloppe géographique Sud Ouest [-62,24, -59,03], Nord Est [-62,15, -58,84]

Couverture taxonomique

Bacteria, profiled by targeting the 16S ssu rRNA gene

Domain  Bacteria (Bacteria)

Archaea, profiled by targeting the 16S ssu rRNA gene

Domain  Archaea (Archaea)

Fungi, profiled by targeting ITS gene

Phylum  Fungi (Fungi)

Données sur le projet

Pas de description disponible

Titre Microbiome (Archaea, Bacteria and Fungi) in soils from King George Island (Antarctica)
Financement This work was supported by the National Key R&D Program of China (2018YFC1406700), the R&D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People’s Republic of China (Grant No. NIMR-2017-8), the National Natural Science Foundation of China (Grant No. 31270538), and the Chinese Polar Scientific Strategy Research Fund IC201706.

Les personnes impliquées dans le projet:

Yumin Zhang

Méthodes d'échantillonnage

Soils were sampled from the A-horizon (10 cm) at an internal distance of approximately 3–5 m, and samples were collected in triplicate around each quadrat plot. Soil samples collected for each replicate were taken from five soil cores (5 cm diameter) and mixed thoroughly. A total of 36 soil samples were placed in sterile plastic bags, and soil DNA was extracted within 2 h in the laboratory of the Great Wall Station. The remaining soils were stored in the freezer until further soil physico-chemical property analyses were performed.

Etendue de l'étude The 12 permanent quadrat plots (1.5 m × 1.0 m each) investigated in this study were established on the Fildes Peninsula and Ardley Island between 2013 and 2015. Each quadrat plot was fenced to minimize disturbance. The distance between quadrat plots ranges from approximately 1.6 to 8.2 km. Sampling occurred during China’s 33rd Antarctic expedition in January 2017.

Description des étapes de la méthode:

  1. The bacterial hypervariable V4 region of the 16S rRNA genes was amplified using primers 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) with a 7-nucleotide barcode and 907R (5’-CCGTCAATTCMTTTRAGTTT-3’). Amplifications of the bacterial 16S rRNA genes were performed, consisting of an initial denaturation at 98 °C for 30 s, followed by 25 cycles of denaturation at 98 °C for 15 s, annealing at 50 °C for 30 s, extension at 72 °C for 30 s, and a final extension at 72 °C for 5 min.
  2. The archaeal V5-6 region of 16S rRNA genes was amplified using primers 524F-10-extF (5’-TGYCAGCCGCCGCGGTAA-3’) with a 7-nucleotide barcode and Arch958-modR (5’-YCCGGCGTTGAVTCCAATT-3’). Amplifications of the archaeal 16S rRNA genes were performed, consisting of an initial denaturation at 95 °C for 30 s, followed by 25 cycles of denaturation at 95 °C for 15 s, annealing at 55 °C for 30 s, extension at 72 °C for 30 s, and a final extension at 72 °C for 5 min.
  3. The fungal rDNA ITS1-5.8S-ITS2 region was amplified using primers ITS5 (5’-GGAAGTAAAAGTCGTAACAAGG-3’) with a 7-nucleotide barcode and ITS4 (5’-TCCTCCGCTTATTGATATGC-3’). Amplifications of the fungal ITS regions were performed, consisting of an initial denaturation at 95 °C for 30 s, followed by 25 cycles of denaturation at 95 °C for 15 s, annealing at 50 °C for 30 s, extension at 72 °C for 30 s, and a final extension at 72 °C for 5 min. The PCR 25 μl reaction mixture contained 0.25 μl Q5 high-fidelity DNA polymerase (NEB), 5 μl reaction buffer, 5 μl high GC buffer, 0.5 μl of 10 mM dNTP, 1 μl template DNA, 1 μl of each primer (10 μM), and 11.25 μl ddH2O.
  4. PCR products were purified using an AxyPreDNA Gel Extraction Kit (Axygen Biosciences, Corning, NY, USA) according to the manufacturer’s instructions. The purified PCR amplicons from each sample were then mixed after quantification using a Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) in the Microplate reader (Bio Tek, FLx800). Sequencing was performed on the Illumina Miseq Platform.

Citations bibliographiques

  1. Zhang, Y., Lu, L., Chang, X., Jiang, F., Gao, X., Yao, Y., ... & Peng, F. (2018). Small-scale soil microbial community heterogeneity linked to landform historical events on King George Island, maritime Antarctica. Frontiers in microbiology, 9, 3065.

Métadonnées additionnelles

Identifiants alternatifs 0e3185d2-7264-4487-b77a-b559de2f2a79
https://ipt.biodiversity.aq/resource?r=microbiome_soil_king_george_island_antarctica