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Global biogeography of desert cyanobacteria

Citation

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, Sweetlove M (2019). Global biogeography of desert cyanobacteria. Version 1.4. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/r3ndq1 accessed via GBIF.org on 2023-03-25.

Description

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

Sampling Description

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).

Sampling

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.

Method steps

  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.

Taxonomic Coverages

Bacteria (16S ssu rRNA) and Cyanobacteria (nifH)
  1. Bacteria
    common name: Bacteria rank: domain
  2. Cyanobacteria
    common name: Cyanobacteria rank: phylum

Geographic Coverages

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

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. -

Contacts

Donnabella Lacap-bugler
originator
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 author
position: Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
Brussels
1000
email: msweetlove@naturalsciences.be
Donnabella Lacap-bugler
administrative point of contact
Auckland University of Technology
Auckland
NZ
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