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Soil microbiome (Bacteria) on Keller Peninsula (Antarctica)
Citation
Roesch L, Fulthorpe R, Pereira A, Pereira C, Lemos L, Barbosa A, Suleiman A, Gerber A, Pereira M, Loss A, de Costa E (2019): Soil microbiome (Bacteria) on Keller Peninsula (Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antarctic_soil_microbiome_keller_peninsula&v=1.1 https://doi.org/10.15468/tjxx17
Contact: Roesch, Luiz Fernando Wurdig

Access data
Archived data
Availability: Creative Commons License This dataset is licensed under a Creative Commons Attribution 4.0 International License.

Description
Amplicon sequencing dataset (454 pyrosequencing and Ion Torrent) of Bacteria (16S ssu rRNA gene) in ice-free soils of Keller Peninsula (Antarctica). more

A total of 12 soil samples were chosen for sampling and were taken from a variety of plant communities having different soil features. Soil was collected removing the plant cover and taking cores of 5 cm diameter and 5 cm depth. All soil was stored on ice upon collection and transported to the laboratory for extraction.
Study Extent: Soil samples were collected on the Keller Peninsula, King George Island, Antarctica during the austral summer of 2009–2010.
Method step description:
  1. DNA was isolated from at least 1 g of mixed soil using the PowerSoilTM DNA Isolation Kit (MO BIO) as described by the manufacturer. The genomic DNA concentration and purity were determined by spectrophotometry.
  2. Twelve independent PCR reactions were performed for each soil sample with the primers 338R and 27F for the amplification of the V1–V2 hypervariable regions of the 16S rRNA gene. PCR was performed with the GoTaq PCR core system (Promega, Madi- son, WI, USA). The mixtures contained 5 ul of 10× PCR buffer, 200 mM dNTPs, 100 mM of each primer, 2.5 U of Taq polymerase and approximately 100ng of DNA template in a final volume of 50 ul. The PCR conditions were 94 ◦ C for 2 min, 30 cycles of 94◦C for 45s; 55◦C for 45s; and 72◦C for 1min extension; followed by 72 ◦C for 6 min. The 16S rRNA gene fragments were sequenced using 454 GS FLX Titanium (Lib-L) chemistry for unidirectional sequencing of the amplicon libraries. Barcoded primers were used to multiplex the amplicon pools so they could be sequenced together and computationally separated afterward. To do this, 8-base barcodes were added to the 5′-end of the reverse primers using the self-correcting barcode method of Hamady et al. (2008). The primers were attached to the GS FLX Titanium Primer A (5′ -CCATCTCATCCCTGCGTGTCTCCGACTCAG-3′ ) and Primer B (5′ - CCTATCCCCTGTGTGCCTTGGCAGTC-3′ ) sequences, modified for use with GS FLX Titanium emPCR Kits (Lib-L) and a two-base linker sequence was inserted between the 454 adapter and the 16S rRNA primers to reduce any effect the composite primer might have on PCR efficiency. The PCR products for each of the 12 samples were purified and combined in equimolar ratios with the quantitative DNA binding method (SequalPrep Kit, Invitrogen, Carlsbad, CA, USA) to create a DNA pool that was used for pyrosequencing from the A-Key adaptor.

Scope
Keywords:
Terrestrial, Dna sequencing, Metadata, Rrna, Antarctica, Bacteria

Geographical coverage
Antarctica Stations [Marine Regions]
Keller Peninsula

Temporal coverage
2009 - 2010

Taxonomic coverage
Bacteria [WoRMS]

Parameter
Molecular data

Contributors
Federal University of Pampa (UNIPAMPA)data creator
Roesch, Luiz Fernando Wurdig
Pereira, Antonio
Pereira, Clarissa
Lemos, Leondro
Barbosa, Anthony
Suleiman, Afnan
University of Torontodata creator
Fulthorpe, Roberta
Unidade de Genômica Computacional Darcy Fontoura de Almeida (UGCDFA)data creator
Gerber, Alexandra
Federal Rural University of Rio de Janeiro (UFRRJ)data creator
Pereira, Marcos
Loss, Arcangelo
de Costa, Elias

Related datasets
Published in:
AntOBIS: Antarctic Ocean Biodiversity Information System
(Partly) included in:
RAS: Register of Antarctic Species

Dataset status: Completed
Data type: Metadata
Data origin: Research: field survey
Metadatarecord created: 2019-04-08
Information last updated: 2019-04-10
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