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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, Sweetlove M (2019). Soil microbiome (Bacteria) on Keller Peninsula (Antarctica). Version 1.1. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/tjxx17 accessed via GBIF.org on 2023-02-04.

Description

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

Sampling Description

Study Extent

Soil samples were collected on the Keller Peninsula, King George Island, Antarctica during the austral summer of 2009–2010.

Sampling

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.

Method steps

  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.

Taxonomic Coverages

Bacteria, based on the 16S ssu rRNA gene
  1. Bacteria
    common name: Bacteria rank: domain

Geographic Coverages

Keller Peninsula, Antarctica

Bibliographic Citations

  1. Roesch, L. F., Fulthorpe, R. R., Pereira, A. B., Pereira, C. K., Lemos, L. N., Barbosa, A. D., ... & da Costa, E. M. (2012). Soil bacterial community abundance and diversity in ice-free areas of Keller Peninsula, Antarctica. Applied soil ecology, 61, 7-15.|Rampelotto, P. H., Barboza, A. D. M., Pereira, A. B., Triplett, E. W., Schaefer, C. E. G., de Oliveira Camargo, F. A., & Roesch, L. F. W. (2015). Distribution and interaction patterns of bacterial communities in an ornithogenic soil of Seymour Island, Antarctica. Microbial ecology, 69(3), 684-694. -

Contacts

Luiz Roesch
originator
Universidade Federal do Pampa
Sao Gabriel
BR
Roberta Fulthorpe
originator
University of Toronto at Scarborough
Scarborough
CA
Antonio Pereira
originator
Universidade Federal do Pampa
Sao Gabriel
BR
Clarissa Pereira
originator
Universidade Federal do Pampa
Sao Gabriel
BR
Leondro Lemos
originator
Universidade Federal do Pampa
Sao Gabriel
BR
Anthony Barbosa
originator
Universidade Federal do Pampa
Sao Gabriel
BR
Afnan Suleiman
originator
Universidade Federal do Pampa
Sao Gabriel
BR
Alexandra Gerber
originator
Unidade de Genômica Computacional Darcy Fontoura de Almeida
Rio de Janeiro
BR
Marcos Pereira
originator
Universidade Federal Rural do Rio de Janeiro
Rio de Janeiro
BR
Arcangelo Loss
originator
Universidade Federal Rural do Rio de Janeiro
Rio de Janeiro
BR
Elias de Costa
originator
Universidade Federal Rural do Rio de Janeiro
Rio de Janeiro
BR
Maxime Sweetlove
metadata author
position: research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
Brussels
1000
BE
email: msweetlove@naturalsciences.be
Luiz Roesch
administrative point of contact
Universidade Federal do Pampa
Sao Gabriel
BR
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