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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 (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 https://doi.org/10.15468/r3ndq1

Access data
Archived data
Availability: Creative Commons License This dataset is licensed under a Creative Commons Attribution 4.0 International License.

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

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.

Scope
Keywords:
Terrestrial, Dna sequencing, Metadata, Antarctica, Victoria Land, McMurdo Dry Valleys, Asia, China, PN, Arctic, Bacteria, Cyanobacteria

Geographical coverage
Antarctica, Victoria Land, McMurdo Dry Valleys [Marine Regions]
Asia, China Stations [Marine Regions]
Tibetan Plateau and Taklimakan Desert
PN, Arctic Stations [Marine Regions]
Devon Island, Canada

Taxonomic coverage
Bacteria [WoRMS]
Cyanobacteria [WoRMS]

Parameter
Molecular data

Contributors
University of Waikato, moredata creator
Kanazawa University, moredata creator
National Aeronautics and Space Administration (NASA), moredata creator
Consejo Superior de Investigaciones Científicas; Museo Nacional de Ciencias Naturales (MNCN), moredata creator
Royal Agricultural University, moredata creator

Related datasets
Published in:
AntOBIS: Antarctic Ocean Biodiversity Information System, more
(Partly) included in:
RAS: Register of Antarctic Species, more

Dataset status: Completed
Data type: Metadata
Data origin: Research: field survey
Metadatarecord created: 2019-04-03
Information last updated: 2019-04-10
All data in the Integrated Marine Information System (IMIS) is subject to the VLIZ privacy policy