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

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Researchers should cite this work as follows:

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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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

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This resource has been registered with GBIF, and assigned the following GBIF UUID: 0e3185d2-7264-4487-b77a-b559de2f2a79.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Metadata

Contacts

Geographic Coverage

Fildes region on the King George island, Antarctica

Taxonomic Coverage

Bacteria, profiled by targeting the 16S ssu rRNA gene

Archaea, profiled by targeting the 16S ssu rRNA gene

Fungi, profiled by targeting ITS gene

Project Data

No Description available

The personnel involved in the project:

Sampling Methods

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.

Method step description:

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.

Bibliographic Citations

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.

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