We’re sorry, but GBIF doesn’t work properly without JavaScript enabled.
Our website has detected that you are using an outdated insecure browser that will prevent you from using the site. We suggest you upgrade to a modern browser.
{{nav.loginGreeting}}
  • Get data
      • Occurrences
      • GBIF API
      • Species
      • Datasets
      • Occurrence snapshots
      • Hosted portals
      • Trends
  • How-to
    • Share data

      • Quick-start guide
      • Dataset classes
      • Data hosting
      • Standards
      • Become a publisher
      • Data quality
      • Data papers
    • Use data

      • Featured data use
      • Citation guidelines
      • GBIF citations
      • Citation widget
  • Tools
    • Publishing

      • IPT
      • Data validator
      • Scientific Collections
      • Suggest a dataset
      • New data model ⭐️
    • Data access and use

      • Hosted portals
      • Data processing
      • Derived datasets
      • rgbif
      • pygbif
      • MAXENT
      • Tools catalogue
    • GBIF labs

      • Species matching
      • Name parser
      • Sequence ID
      • Relative observation trends
      • GBIF data blog
  • Community
    • Network

      • Participant network
      • Nodes
      • Publishers
      • Network contacts
      • Community forum
      • alliance for biodiversity knowledge
    • Volunteers

      • Mentors
      • Ambassadors
      • Translators
      • Citizen scientists
    • Activities

      • Capacity enhancement
      • Programmes & projects
      • Training and learning resources
      • Data Use Club
      • Living Atlases
  • About
    • Inside GBIF

      • What is GBIF?
      • Become a member
      • Governance
      • Implementation plan
      • Work Programme
      • Funders
      • Partnerships
      • Release notes
      • Contacts
    • News & outreach

      • News
      • Newsletters and lists
      • Events
      • Ebbe Nielsen Challenge
      • Graduate Researchers Award
      • Science Review
      • Data use
  • User profile

Bacteria on mummified seals in the Antarctic Dry Valleys

Citation

Tiao G, Lee C, McDonald I, Cowan D, Cary C, Sweetlove M (2019). Bacteria on mummified seals in the Antarctic Dry Valleys. Version 1.2. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/o1km7d accessed via GBIF.org on 2023-02-07.

Description

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

Sampling Description

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)

Sampling

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.

Method steps

  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).

Taxonomic Coverages

Amplicin sequencing of Bacteria (16S ssu rRNA gene)
  1. Bacteria
    common name: Bacteria rank: domain

Geographic Coverages

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.

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. -

Contacts

Grace Tiao
originator
University of Waikato
Hamilton
NZ
Charles Lee
originator
University of Waikato
Hamilton
NZ
Ian McDonald
originator
University of Waikato
Hamilton
NZ
Donald Cowan
originator
University of the Western Cape
Cape Town
ZA
Craig Cary
originator
University of Waikato
Hamilton
NZ
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
Brussels
1000
email: msweetlove@naturalsciences.be
Grace Tiao
administrative point of contact
University of Waikato
Hamilton
NZ
What is GBIF? API FAQ Newsletter Privacy Terms and agreements Citation Code of Conduct Acknowledgements
Contact GBIF Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø Denmark