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

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Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

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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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: 0e3185d2-7264-4487-b77a-b559de2f2a79.  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

Cobertura Geográfica

Fildes region on the King George island, Antarctica

Cobertura Taxonômica

Bacteria, profiled by targeting the 16S ssu rRNA gene

Archaea, profiled by targeting the 16S ssu rRNA gene

Fungi, profiled by targeting ITS gene

Dados Sobre o Projeto

Nenhuma descrição disponível

O pessoal envolvido no projeto:

Métodos de Amostragem

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.

Descrição dos passos do método:

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.

Citações bibliográficas

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.

Metadados Adicionais