Bacteria on mummified seals in the Antarctic Dry Valleys

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

Amplicon dataset of Bacteria (16S ssu rRNA) living around mummified seal carcasses in the Antarctic Dry Valleys

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How to cite

Researchers should cite this work as follows:

Tiao G, Lee C, McDonald I, Cowan D, Cary C (2019): Bacteria on mummified seals in the Antarctic Dry Valleys. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antarctic_dry_valley_mummified_seal_microbiome&v=1.2

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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: a3fb3af6-724d-4de3-ace8-4fa21cc729ed.  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:

Grace Tiao
University of Waikato Hamilton NZ
Charles Lee
University of Waikato Hamilton NZ
Ian McDonald
University of Waikato Hamilton NZ
Donald Cowan
University of the Western Cape Cape Town ZA
Craig Cary
University of Waikato Hamilton NZ

Who can answer questions about the resource:

Grace Tiao
University of Waikato Hamilton NZ

Who filled in the metadata:

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

Who else was associated with the resource:

User

Geographic Coverage

soil samples from under and around mummified crabeater seal near Lake Miers (S 78°05′36″, E 163°51′22″), Miers Valley, Victoria Land, Antarctica, that was transported to a similar site 20 m north.

Bounding Coordinates South West [-78.933, 163.856], North East [-78.933, 163.856]

Taxonomic Coverage

Amplicin sequencing of Bacteria (16S ssu rRNA gene)

Domain  Bacteria (Bacteria)

Temporal Coverage

Start Date / End Date 2005-01-15 / 2009-01-15

Project Data

No Description available

Title Seal Movement
Funding This work was supported through grants from the New Zealand Foundation for Research Science and Technology, Antarctica New Zealand, and the National Science Foundation (OPP-0739648 and 0944560). Additional support was provided by a George Peabody Gardner Fellowship, by the New Zealand Foundation for Research, Science and Technology Postdoctoral Research Fellowship and the New Zealand Marsden Foundation (UOW1003).

The personnel involved in the project:

Grace Tiao

Sampling Methods

Soil samples (>10 g each) were collected aseptically at a depth of 0.05m. Samples were stored in sterile plastic containers at −80 °C until analysis.

Study Extent On 30 January 2006, a mummified crabeater seal was carried from its original resting site near Lake Miers (S 78°05′36″, E 163°51′22″), Miers Valley, Victoria Land, Antarctica, to a new site of similar geomorphology 20 m north. Samples for amplicon sequencing were taken from the original site before transportation (austral summer 2005), the new site before transportation (control, austral summer 2006), and the new site after incubation (austral summer 2009)

Method step description:

  1. 16S rRNA gene were generated using the primer pair Tx9 (5′-GGATTAGAWACCCBGGTAGTC-3′) and 1391R (5′-GACGGGCRGTGWGTRCA-3′). PCR was performed in triplicate and pooled to reduce stochastic variability between reactions. Each 30 μl reaction contained 5 or 20 ng of extracted community DNA, Pfx polymerase and platinum polymerase (0.5 U each; Invitrogen), 1× Pfx PCR buffer with Pfx enhancer, 0.2 mM dNTPs, 1 mM MgCl2, 0.02 mg ml−1 BSA, 0.8 μM of forward and reverse primer, and PCR-grade water. Thermal cycling conditions were 94 °C for 2 min; 18 or 24 cycles of 94 °C for 15 s, 55 °C for 30 s and 68 °C for 1 min; and 68 °C for 3 min.
  2. Amplicons were size-selected and purified using polyacrylamide gel electrophoresis before being prepared for pyrosequencing by Taxon Biosciences (Tiburon, CA, USA).

Bibliographic Citations

  1. Tiao, G., Lee, C. K., McDonald, I. R., Cowan, D. A., & Cary, S. C. (2012). Rapid microbial response to the presence of an ancient relic in the Antarctic Dry Valleys. Nature Communications, 3, 660.

Additional Metadata

Alternative Identifiers a3fb3af6-724d-4de3-ace8-4fa21cc729ed
https://ipt.biodiversity.aq/resource?r=antarctic_dry_valley_mummified_seal_microbiome