Soil microbiome (Bacteria) on Keller Peninsula (Antarctica)

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Researchers should cite this work as follows:

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

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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: 48350841-8927-4c78-bbc1-24c01a4d5586.  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

Geographic Coverage

Keller Peninsula, Antarctica

Taxonomic Coverage

Bacteria, based on the 16S ssu rRNA gene

Temporal Coverage

Project Data

No Description available

The personnel involved in the project:

Sampling Methods

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 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.

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.

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