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Bacteria and Archaea in different soil types on King George Island (South Shetland Islands, Antarctica)

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (454 pyrosequencing) of Bacteria and Archaea (16S ssu rRNA gene) in three sets of environmentally distinct soil samples on King George Island (Antarctica)

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How to cite

Researchers should cite this work as follows:

Pershina E, Ivanova E, Abakumov E, Andronova E (2019): Bacteria and Archaea in different soil types on King George Island (South Shetland Islands, Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacteria_and_archaea_in_different_king_george_island_soils&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: 84d7d83b-94d2-4d44-a541-2c9e51e0f972.  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

Who created the resource:

E. Pershina
All-Russia Research Institute for Agricultural Microbiology St. Petersburg RU
E. Ivanova
All-Russia Research Institute for Agricultural Microbiology St. Petersburg RU
E. Abakumov
St. Petersburg State University St. Petersburg RU
E. Andronova
All-Russia Research Institute for Agricultural Microbiology St. Petersburg RU

Who can answer questions about the resource:

E. Pershina
All-Russia Research Institute for Agricultural Microbiology St. Petersburg RU

Who filled in the metadata:

Maxime Sweetlove
Research assistent
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels BE

Who else was associated with the resource:

User

Geographic Coverage

King George Island (Southern Shetland Islands:Antarctica)

Bounding Coordinates South West [-62.276, -59.032], North East [-62.113, -58.938]

Taxonomic Coverage

Bacteria and Archaea (16S ssu rRNA gene, v4 region)

Domain  Bacteria (Bacteria),  Archaea (Archaea)

Temporal Coverage

Start Date / End Date 2016-01-22 / 2016-02-02

Project Data

No Description available

Title Soil biota dynamics in chronoseries of post-technogenic landscapes: analyses of soil ecological effectiveness of ecosystems restoration
Funding This work was supported by the Russian Scientific Foundation projects 17-16-01030, ‘Soil biota dynamics in chronoseries of post-technogenic landscapes: analyses of soil ecological effectiveness of ecosystems restoration’ (soil sampling, agrochemical analysis, preparation of the manuscript), and 14-26-00094 P, ‘Analysis of the soil microbiomes’ genetic and evolutionary potential for increasing plant productivity and soil fertility’ (molecular analysis, pyrosequencing, bioinformatics).

The personnel involved in the project:

E. Pershina

Sampling Methods

Soil samples (50 g) were collected from five points at each site by the ‘envelope method’ (four points in the corners of the square and one in the centre). All samples were homogenized, and five subsamples of 0.2 g each were used for the DNA extractions.

Study Extent Soils samples were taken from King George Island (Fildes Peninsula) and Nelson Island during the 61st Russian Antarctic expedition in 2016.

Method step description:

  1. Following the manufacturer’s instructions, DNA was extracted from the 0.2 g soil samples using the PowerSoil DNA Isolation Kit (Mobio Laboratories, Solana Beach, CA, USA), which included a bead-beating step. The samples were homogenized twice using a Precellys 24 tissue homogenizer (Bertin Corp, USA) for 30 s at 6.5 m s-1. The purity and quantity of the DNA were tested by electrophoresis in 0.5 × TAE buffer on 1% agarose gels. DNA concentrations were measured at 260nm using a SPECTROStar Nano microplate reader (BMG Labtech, Ortenberg, Germany). The average DNA yield was 2–5 μg at concentrations of 10–50 ng μL-1. The purified DNA templates were amplified with the universal multiplex primers F515 5′-GTGCCAGCMGCCGCGGTAA-3′ and R806 5′-GGACTACVSGGGTATCTAAT-3′ (Bates et al. 2011), which target the variable V4 region of bacterial and archaeal 16S rRNA genes. Each multiplex primer contained the adapter, a 4 bp key (TCAG), a 10 bp barcode, and the primer sequences. The amplified product was expected to be 400 bp long. The purification, pooling and pyrosequencing of the amplicons were performed with specified reagents according to the manufacturer’s instructions (Roche, Branford, USA). Pyrosequencing was performed with a Roche 454 GS Junior system in the Core Centrum ‘Genomic Technologies, Proteomics and Cell Biology’ (All-Russia Research Institute for Agricultural Microbiology).

Bibliographic Citations

  1. Pershina, E. V., Ivanova, E. A., Abakumov, E. V., & Andronov, E. E. (2018). The impacts of deglaciation and human activity on the taxonomic structure of prokaryotic communities in Antarctic soils on King George Island. Antarctic Science, 30(5), 278-288.

Additional Metadata

Alternative Identifiers 84d7d83b-94d2-4d44-a541-2c9e51e0f972
https://ipt.biodiversity.aq/resource?r=bacteria_and_archaea_in_different_king_george_island_soils