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Microbiome (Bacteria, Archaea and fungi) from University Valley Permafrost cores (Antarctica)

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

Amplicon sequencing dataset (Bacteria and Archaea based on 16S ssu rRNA gene, Fungi and other eukaryotes, based on the ITS marker) of microorganisms in permafrost samples (two cores with three different depths) taken in University Valley, Antarctica.

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How to cite

Researchers should cite this work as follows:

Goordial J, Davila A, Lacelle D, Pollard W, Marinova M, Greer C, DiRuggiero J, McKay C, Whyte L (2019): Microbiome (Bacteria, Archaea and fungi) from University Valley Permafrost cores (Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbiome_university_valley_permafrost_antarctica&v=1.1

Rights

Researchers should respect the following rights statement:

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: 3d255a2a-c297-4588-b67c-e0c2b4a31709.  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:

Jacqueline Goordial
McGill University Ste-Anne-de-Bellevue CA
Alfonso Davila
NASA Ames Research Center Moffett Field US
Denis Lacelle
University of Ottawa Ottawa CA
Wayne Pollard
McGill University Montreal CA
Margarita Marinova
NASA Ames Research Center Moffett Field US
Charles Greer
National Research Council Canada Montreal CA
Jocelyn DiRuggiero
The Johns Hopkins University Baltimore US
Christopher McKay
NASA Ames Research Center Moffett Field US
Lyle Whyte
McGill University Ste-Anne-de-Bellevue CA

Who can answer questions about the resource:

Jacqueline Goordial
McGill University Ste-Anne-de-Bellevue CA

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

University Valley, McMurdo Dry Valleys, Antarctica

Bounding Coordinates South West [-77.864, 160.729], North East [-77.864, 160.729]

Taxonomic Coverage

Bacteria were profiled by targeting the 16S ssu rRNA gene

Domain  Bacteria (Bacteria)

Archaea were profiled by targeting the 16S ssu rRNA gene

Domain  Archaea (Archaea)

Fungi (and some other Eukaryote groups) were profiled by targeting the ITS marker

Phylum  Fungi (Fungi)

Project Data

No Description available

Title Microbiome (Bacteria, Archaea and fungi) from University Valley Permafrost cores (Antarctica)
Funding This work was supported by NASA ASTEP program and with field support via NSF/OPP (project B-302-M). Support was provided by the Natural Sciences and Engineering Research Council (NSERC) Discovery Grant Program, NSERC Northern Supplements Program and NSERC CREATE Canadian Astrobiology Training Program (CATP).

The personnel involved in the project:

Jacqueline Goordial

Sampling Methods

University Valley permafrost core samples were collected with a SIPRE corer (USA Cold Regions Research and Engineering Laboratory, Hanover, NH, USA). The cores were 0.3 km apart from each other. Samples were shipped to McGill University in a thermally insulated box and maintained at −20 °C until processing. All sample handling and processing were carried out according to protocols developed for low biomass permafrost soils to minimize contamination. Initial core processing took place in a walk-in freezer held at −5 °C in a dedicated laminar flow hood where 1 cm of the outside of the core was removed with a sterilized chisel. An additional 1 cm of the outside core was removed in a biological safety cabinet at room temperature immediately before samples being weighed and aliquoted for analysis. Dedicated biological safety cabinets, which had been pretreated to remove DNA/RNA or cells, were used for sample processing, nucleic acid extraction and PCR preparation.

Study Extent Samples were taken in December 2009 from permafrost soils in University Valley (1650–1800 m above sea level (a.s.l.)), located 450 m above Beacon Valley in the Quartermain Range. Samples analysed in this study were located near the head of the valley close to the glacier, a shadowed region where the soil surface experiences few thaw hours, and where the uppermost 50 cm of ice content in the ice-cemented permafrost formed from water vapour diffusion into the cryotic soils rather than from liquid water.
Quality Control Negative controls (H2O in place of soil) underwent identical handling during the extraction procedure and were used as templates for PCR using 16S rRNA gene primers (27 F and 1492 R) to ensure no contamination during extraction.

Method step description:

  1. Community DNA was extracted from 2 g of permafrost soil using the UltraClean Soil DNA Isolation kit (MoBio Laboratories Inc., Carlsbad, CA, USA), as described in the alternative protocol for maximum yield, and a bead beating step was added to aid lysis. For each sample, five extractions were performed and the resulting DNA was pooled and concentrated.
  2. DNA was sent for small subunit rDNA pyrosequencing analyses at the Research and Testing Laboratory (Lubbock, TX, USA) using the Roche 454 GS-FLX platform (Roche 454, Branford, CT, USA). Sample libraries were prepared with the following primers for bacterial 16S rRNA gene (28F-5′-GAGTTTGATCNTGGCTCAG-3′, 519R-5′-GTNTTACNGCGGCKGCTG-3′), archaeal 16S rRNA gene (349F-5′-GYGCASCAGKCGMGAAW-3′, 806R-5′-GGACTACVSGGGTATCTAAT-3′), Eukaryal/fungal internal transcribed region (ITS) (ITS1F-5′-CTTGGTCATTTAGAGGAAGTAA-3′, ITS4R-5′-TCCTCCGCTTATTGATATGC-3′) genes.

Bibliographic Citations

  1. Goordial, J., Davila, A., Lacelle, D., Pollard, W., Marinova, M. M., Greer, C. W., ... & Whyte, L. G. (2016). Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica. The ISME journal, 10(7), 1613.

Additional Metadata

Alternative Identifiers 3d255a2a-c297-4588-b67c-e0c2b4a31709
https://ipt.biodiversity.aq/resource?r=microbiome_university_valley_permafrost_antarctica