Antarctic Surface Snow Bacterial Communities

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 29, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (Illumina MiSeq) of Bacteria (16S ssu rRNA) in surface snow collected between the South Orkney Islands and the Ellsworth Mountains between December 2012 and January 2014.

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Researchers should cite this work as follows:

Malard L, Sabacka M, Magiopoulos I, Mowlem M, Hodson A, Tranter M, Siegert M, Pearce D (2019): Antarctic Surface Snow Bacterial Communities. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antarctic_surface_snow_bacterial_communities&v=1.0

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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.

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This resource has been registered with GBIF, and assigned the following GBIF UUID: f9644d4b-3c39-4147-9d84-4baff93e1737.  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:

Lucie Malard
Northumbria University at Newcastle Newcastle upon Tyne GB
Marie Sabacka
University of South Bohemia in České Budějovice České Budějovice CZ
Iordanis Magiopoulos
Hellenic Centre for Marine Research Heraklion GR
Matt Mowlem
National Oceanography Centre Southampton Southampton GB
Andy Hodson
University Centre in Svalbard Longyearbyen NO
Martyn Tranter
University of Bristol Bristol GB
Martin Siegert
Imperial College London London GB
David Pearce
Northumbria University at Newcastle Newcastle upon Tyne GB

Who can answer questions about the resource:

Lucie Malard
Northumbria University at Newcastle Newcastle upon Tyne GB

Who filled in the metadata:

Maxime Sweetlove
Research assistant
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels

Who else was associated with the resource:

User

Geographic Coverage

The region between the South Orkney Islands and the Ellsworth Mountains (Antarctica)

Bounding Coordinates South West [-78.976, -100], North East [-60.707, -45.593]

Taxonomic Coverage

Bacteria were profiled by targeting the v3-v4 region of the 16S ssu rRNA gene with the primers 341F and 785R

Domain  Bacteria (Bacteria)

Project Data

No Description available

Title Antarctic Surface Snow Bacterial Communities
Funding This work was supported by grants from the United Kingdom Natural Environment Research Council grants G00465X/1, G00465X/2, G00465X/3, NE/H014446/1, and NE/H014802/1 and from the European Commission’s Marie Skłodowska-Curie Actions program under project number 675546.

The personnel involved in the project:

Lucie Malard

Sampling Methods

Snow was collected from the surface to represent collection during melt water production for hot-water drilling. At each sampling location, a 1 m snow pit was excavated and the top 30 cm of snow was sampled using an ethanol sterilized shovel and Whirl-Pak bags (Nasco, WI, United States). Samples were transported to the field laboratory, where they were melted and passed through 0.2 μm Sterivex filters (Merck, Darmstadt, Germany), before freezing at −20°C for transport and processing in the United Kingdom.

Study Extent Snow samples were collected between the South Orkney Islands and the Ellsworth Mountains between December 2012 and January 2014. On Signy Island, two sites were sampled; Gourlay Snowfield and Tuva Glacier. SkyBlu samples came from the vicinity of the BAS blue ice runway (a logistics hub for deep field operations). Camp samples were collected around the kitchen, generator and drilling areas.

Method step description:

  1. SkyBlu, Pine Island Bay and Ellsworth snow samples were processed in two ways; PMA-treated and non-PMA-treated in order to differentiate the potentially viable microbial community from relic DNA. Each 0.2 μm filter was cut in half using sterile and DNAase/ethanol treated razors. For each sample, one-half was processed with PMA as per Nocker and Camper (2009) and Fittipaldi et al. (2012), using a 20 mM stock solution of PMA (Biotium, Hayward, CA, United States) in a 20% (v/v) aqueous solution of dimethyl sulfoxide (DMSO). Filters for PMA treatment were placed in a 6-well plate and a PMA solution at a final concentration of 100 μM was added. Cross-linking was initiated by 10 min incubation on ice, in the dark with occasional mixing, followed by 5 min of light exposure using a 650 W halogen lamp (FLASH 2000 L, DTS, Italy), at a 20 cm distance. The process was carried out in a laminar flow hood to avoid contamination of the samples. Non-PMA-treated samples were incubated in a 20% (v/v) aqueous solution of DMSO, and treated following the same protocol as PMA-treated samples. All samples were washed twice with sterile phosphate buffered saline (PBS) and all samples were then used for DNA extraction. DNA from snow samples was extracted using the PowerWater kit from MoBio (Qiagen, Carlsbad, CA, United States). Each sample was PCR amplified using the primers 341F and 785R covering the V3-V4 regions of the 16S rRNA gene (Klindworth et al., 2013), under the following conditions: initial denaturation at 95°C for 5 min then 25 cycles of 40 s denaturation at 95°C; primer annealing at 55°C for 2 min; and elongation at 72°C for 1 min then a final elongation at 72°C for 7 min (Hodson et al., 2017). DNA extraction kit controls were included alongside the snow derived DNA and sequenced. PCR amplicons were cleaned, normalized, quantified and supplemented with 5% PhiX before being loaded on Illumina MiSeq, as per the Illumina standard operating protocol (Kozich et al., 2013).
  2. DNA from snow samples was extracted using the PowerWater kit from MoBio (Qiagen, Carlsbad, CA, United States). Each sample was PCR amplified using the primers 341F and 785R covering the V3-V4 regions of the 16S rRNA gene, under the following conditions: initial denaturation at 95°C for 5 min then 25 cycles of 40 s denaturation at 95°C; primer annealing at 55°C for 2 min; and elongation at 72°C for 1 min then a final elongation at 72°C for 7 min (Hodson et al., 2017). DNA extraction kit controls were included alongside the snow derived DNA and sequenced. PCR amplicons were cleaned, normalized, quantified and supplemented with 5% PhiX before being loaded on Illumina MiSeq, as per the Illumina standard operating protocol (Kozich et al., 2013).

Bibliographic Citations

  1. Malard, L. A., Šabacká, M., Magiopoulos, I., Hodson, A., Tranter, M., Siegert, M. J., & Pearce, D. A. (2019). Spatial variability of Antarctic surface snow bacterial communities. Frontiers in Microbiology, 10, 461. https://doi.org/10.3389/fmicb.2019.00461