V3-V4 16S rDNA of soil bacteria in King George Island and Deception Island
Citation
Chua C, Yong S, Gonzalez M, Lavin P, Cheah Y, Tan G, Wong C, Sweetlove M (2019). V3-V4 16S rDNA of soil bacteria in King George Island and Deception Island. Version 1.1. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/spzi1j accessed via GBIF.org on 2024-12-13.Description
Amplicon sequencing dataset (Illumina MiSeq 250bp PE) of soil bacteria (16S ssu rRNA gene, v3-v4) on King George Island and Deception Island (Antarctica)Sampling Description
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.Sampling
Samples were stored at –20°C immediately after sampling.Method steps
- 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.
- The concentration and purity of the extracted genomic DNA were measured using the NanoDropTM 2000 spectrophotometer (Thermo Scientific Inc., Waltham, MA, USA).
- 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).
Taxonomic Coverages
Bacteria, 16S ssu rRNA gene, v3-v4 region
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Bacteriacommon name: Bacteria rank: domain
Geographic Coverages
King George Island and Deception Island, Antarctica
Bibliographic Citations
- 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. -
Contacts
C. Chuaoriginator
Universiti Malaysia Sabah
Kota Kinabalu
88400
MY
S. Yong
originator
Universiti Malaysia Sabah
Kota Kinabalu
88400
MY
M. Gonzalez
originator
Instituto Antártico Chileno
Punta Arenas
CL
P. Lavin
originator
Instituto Antártico Chileno
Punta Arenas
CL
Y. Cheah
originator
Universiti Putra Malaysia
Serdang
43400
MY
G. Tan
originator
University of Malaya
Kuala Lumpur
88400
MY
C. Wong
originator
Universiti Malaysia Sabah
Kota Kinabalu
88400
MY
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Institute for Naturals Sciences
Rue Vautier 29
Brussels
1000
email: msweetlove@naturalsciences.be
C. Chua
administrative point of contact
Universiti Malaysia Sabah
Kota Kinabalu
88400
MY
C. Wong
administrative point of contact
Universiti Malaysia Sabah
Kota Kinabalu
88400
MY