Soil microbiome (Bacteria) on Keller Peninsula (Antarctica)

Luiz Roesch1, Roberta Fulthorpe2, Antonio Pereira1, Clarissa Pereira1, Leondro Lemos1, Anthony Barbosa1, Afnan Suleiman1, Alexandra Gerber3, Marcos Pereira4, Arcangelo Loss4, Elias de Costa4, Maxime Sweetlove5

1 Universidade Federal do Pampa, Sao Gabriel, Brazil; 2 University of Toronto at Scarborough, Scarborough, Canada; 3 Unidade de Genômica Computacional Darcy Fontoura de Almeida, Rio de Janeiro, Brazil; 4 Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil; 5 Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000, Brussels, Belgium

Corresponding author(s): Luiz RoeschRoberta FulthorpeAntonio PereiraClarissa PereiraLeondro LemosAnthony BarbosaAfnan SuleimanAlexandra GerberMarcos PereiraArcangelo LossElias de Costa, Maxime Sweetlove (msweetlove@naturalsciences.be)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource 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

Abstract

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

Keywords: Metadata

Project details

Project title: Soil microbiome (Bacteria) on Keller Peninsula (Antarctica)
Personnel: Luiz Roesch
Funding: This work was supported by the INCT-APA (CNPq process No. 574018/2008-5, FAPERJ E-26/170.023/2008) and Ministry of Science and Technology, and the Secretariat for the Marine Resources Interministerial Committee (SECIRM). Additional funding was provided via a fellowships from the CNPq (process number 503370/2009-6).

Data published through GBIF: https://ipt.biodiversity.aq/resource?r=antarctic_soil_microbiome_keller_peninsula

Taxonomic coverage

General taxonomic coverage description: Bacteria, based on the 16S ssu rRNA gene
Taxonomic ranks
Domain: Bacteria
Common names: Bacteria

Spatial coverage

General spatial coverage: Keller Peninsula, Antarctica
Coordinates: 64°17'38.4''S and 62°3'43.2''S Latitude; 58°28'55.2''W and 56°41'27.6''W Longitude 

Formation period: 2009-2010

Methods

Method step description: 
- . 	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.
- . 	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.
Study extent description: Soil samples were collected on the Keller Peninsula, King George Island, Antarctica during the austral summer of 2009–2010.
Sampling description: 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.

Metadata language: English
Date of metadata creation: 2019-02-18
Hierarchy level: Dataset

References
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.