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V3-V4 16S rDNA of soil bacteria in King George Island and Deception Island

Latest version published by SCAR - Microbial Antarctic Resource System on Feb 1, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (Illumina MiSeq 250bp PE) of soil bacteria (16S ssu rRNA gene, v3-v4) on King George Island and Deception Island (Antarctica)

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How to cite

Researchers should cite this work as follows:

Chua C, Yong S, Gonzalez M, Lavin P, Cheah Y, Tan G, Wong C (2019): V3-V4 16S rDNA of soil bacteria in King George Island and Deception Island. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. http://ipt.biodiversity.aq/resource?r=soil_bacteria_king_george_island_and_deception_island&v=1.0

Rights

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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.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: fca3f5da-a6ae-464d-a488-38439546056d.  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

Who created the resource:

C. Chua
Universiti Malaysia Sabah 88400 Kota Kinabalu MY
S. Yong
Universiti Malaysia Sabah 88400 Kota Kinabalu MY
M. Gonzalez
Instituto Antártico Chileno Punta Arenas CL
P. Lavin
Instituto Antártico Chileno Punta Arenas CL
Y. Cheah
Universiti Putra Malaysia 43400 Serdang MY
G. Tan
University of Malaya 88400 Kuala Lumpur MY
C. Wong
Universiti Malaysia Sabah 88400 Kota Kinabalu MY

Who can answer questions about the resource:

C. Chua
Universiti Malaysia Sabah 88400 Kota Kinabalu MY
C. Wong
Universiti Malaysia Sabah 88400 Kota Kinabalu MY

Who filled in the metadata:

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Naturals Sciences Rue Vautier 29 1000 Brussels

Who else was associated with the resource:

User

Geographic Coverage

King George Island and Deception Island, Antarctica

Bounding Coordinates South West [-62.99, -60.68], North East [-62.19, -58.94]

Taxonomic Coverage

Bacteria, 16S ssu rRNA gene, v3-v4 region

Domain  Bacteria (Bacteria)

Project Data

No Description available

Title V3-V4 16S rDNA of soil bacteria in King George Island and Deception Island
Funding his work was supported by the Ministry of Science, Technology and Innovation (MOSTI), Malaysia under the Flagship project FP0712E012.

The personnel involved in the project:

C. Chua

Sampling Methods

Samples were stored at –20°C immediately after sampling.

Study Extent Soil samples were collected from King George Island (S62°11′35.3′′; W58°56′6.2′′) and Deception Island (S62°59′023′′; W60°40′51.7′′), Antarctica in February 2007.

Method step description:

  1. Total bacterial genomic DNA was extracted from soils using the method described in Zhou et al. (1996) DNA recovery from soils of diverse composition. Appl. Environ. Microbiol., 62(2), 316–322.
  2. The concentration and purity of the extracted genomic DNA were measured using the NanoDropTM 2000 spectrophotometer (Thermo Scientific Inc., Waltham, MA, USA).
  3. The V3–V4 region of the bacterial 16S rRNA gene was amplified using locus-specific primers, S-DBact-0341-b- S-17 (5′-TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCT ACG GGN GGC WGC AG-3′)and S-D-Bact-0785-a-A-21 (5′-GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA CTA CHV GGG TAT CTA ATC C-3′). The 16S rDNA amplicons were subjected to paired-end sequencing on Illumina MiSeq platform using 2 × 250 bp MiSeq Reagent Kit v2 (Illumina® Inc., San Diego, California).

Bibliographic Citations

  1. Chua, C. Y., Yong, S. T., González, M. A., Lavin, P., Cheah, Y. K., Tan, G. Y. A., & Wong, C. M. V. L. (2018). Analysis of bacterial communities of King George and Deception Islands, Antarctica using high-throughput sequencing. CURRENT SCIENCE, 115(9), 1701.