Global biogeography of desert cyanobacteria

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019 SCAR - Microbial Antarctic Resource System
Publication date:
19 March 2019
License:
CC-BY 4.0

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Description

Amplicon sequencing dataset (454 pyrosequencing) of Bacteria (16S ssu rRNA) and Cyanobacteria (nifH) in cold desert quartz rocks

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Lacap-bugler D, Lee K, Archer S, Gillman L, Lau M, Leuzinger S, Lee C, Maki T, McKay C, Perrott J, de los Rios-Murillo A, Warren-Rhodes K, Hopkins D, Pointing S (2018): Global biogeography of desert cyanobacteria. v1.4. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=desert_cyanobacteria&v=1.4

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: 914f39c7-7bb2-4e77-a4ae-36147aa07daf.  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

Donnabella Lacap-bugler
  • Originator
  • Point Of Contact
Auckland University of Technology
Auckland
NZ
Kevin Lee
  • Originator
Auckland University of Technology
Auckland
NZ
Stephen Archer
  • Originator
Auckland University of Technology
Auckland
NZ
Len Gillman
  • Originator
Auckland University of Technology
Auckland
NZ
Maggie Lau
  • Originator
Princeton University
Princeton
US
Sebastian Leuzinger
  • Originator
Auckland University of Technology
Auckland
NZ
Charles Lee
  • Originator
University of Waikato
Hamilton
NZ
Teruya Maki
  • Originator
Kanazawa University
Kanazawa
JP
Christoffer McKay
  • Originator
National Aeronautics and Space Administration Ames Research Center
Moffett Field
US
John Perrott
  • Originator
Auckland University of Technology
Auckland
NZ
Asunción de los Rios-Murillo
  • Originator
Museo Nacional de Ciencias Naturales
Madrid
ES
Kimberley Warren-Rhodes
  • Originator
Kanazawa University
Kanazawa
JP
David Hopkins
  • Originator
The Royal Agricultural University
Cirencester
GB
Stephen Pointing
  • Originator
Auckland University of Technology
Auckland
NZ
Maxime Sweetlove
  • Metadata Provider
Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
1000 Brussels

Geographic Coverage

Tibetan Plateau, China; Taklimakan Desert, China; Devon Island (Arctic), Canada; McMurdo Dry Valleys, Antarctica

Bounding Coordinates South West [-77.41, 88.616], North East [42.715, 161.193]

Taxonomic Coverage

Bacteria (16S ssu rRNA) and Cyanobacteria (nifH)

Domain Bacteria (Bacteria)
Phylum Cyanobacteria (Cyanobacteria)

Project Data

No Description available

Title Global biogeography of desert cyanobacteria
Funding The research was funded by the NASA Astrobiology Science and Technology for Exploring Planets (ASTEP) program and the Institute for Applied Ecology New Zealand (www.aenz.aut.ac.nz).

The personnel involved in the project:

Donnabella Lacab-bugler

Sampling Methods

Colonized quartz stones were retrieved by hand (using isopropyl alcohol surface sterilized latex gloves) and loose soil particles gently removed with a sterile (autoclaved) paintbrush. Samples were then stored in sterile Whirlpak bags (Nasco) at -20°C in the field and in transit, and subsequently stored frozen at -80°C in the laboratory until processed.

Study Extent Hypolithic communities were recovered from quartz substrate in desert pavement on the Tibetan Plateau (China), the Taklimakan Desert (China), Devon Island (Canada) and the McMurdo Dry Valleys (Antarctica).

Method step description:

  1. Amplification of 16S rRNA genes was achieved using primer pair 341F and 907R with PCR conditions involving an initial denaturation time of 5min; 30 cycles at 95°C for 1 min, 55°C for 1 min, 72°C for 1 min, and a final extension at 72°C for 10 min. Positive and negative controls were run for every PCR. For each amplicon library purification was carried out with Agencourt AMPure XP Bead (Beckman Coulter, CA, USA) according to manufacturer’s instructions. The libraries were quantified with Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen Life Technologies, NY, USA) using FLUOstar OPTIMA F fluorometer (BMG Labtech GmbH, Offenburg, Germany) and library quality was assessed with the FlashGel System (Lonza Group Ltd., Basel, Switzerland).
  2. Emulsion-PCR was carried out with GS Junior Titanium emPCR Kit (Lib-L, 454 Life Sciences Corp., CT, USA) according to the emPCR Amplification Method Manual – Lib-L, Single-Prep. The sequencing reaction was carried out with the GS Junior Titanium Sequencing Kit and GS Junior Titanium PicoTiterPlate Kit (454 Life Sciences Corp.) according to the manufacturer’s instructions. The sequencing run was conducted in 200 cycles.

Bibliographic Citations

  1. Lacap-Bugler, D. C., Lee, K. K., Archer, S., Gillman, L. N., Lau, M. C., Leuzinger, S., ... & de los Rios-Murillo, A. (2017). Global diversity of desert hypolithic cyanobacteria. Frontiers in microbiology, 8, 867.

Additional Metadata

Alternative Identifiers 914f39c7-7bb2-4e77-a4ae-36147aa07daf
https://ipt.biodiversity.aq/resource?r=desert_cyanobacteria