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Antarctic Surface Snow Bacterial Communities

Dernière version Publié par SCAR - Microbial Antarctic Resource System le 29 mars 2019 SCAR - Microbial Antarctic Resource System
Date de publication:
29 mars 2019
Licence:
CC-BY 4.0

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Description

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.

Versions

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

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

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : f9644d4b-3c39-4147-9d84-4baff93e1737.  SCAR - Microbial Antarctic Resource System publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Scientific Committee on Antarctic Research.

Mots-clé

Metadata

Contacts

Personne ayant créé cette ressource:
-

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

Personne pouvant répondre aux questions sur la ressource:

Lucie Malard
Northumbria University at Newcastle
Newcastle upon Tyne
GB

Personne ayant renseigné les métadonnées:
-

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

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

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

Enveloppe géographique Sud Ouest [-78,976, -100], Nord Est [-60,707, -45,593]

Couverture taxonomique

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

Domain Bacteria (Bacteria)

Données sur le projet

Pas de description disponible

Titre Antarctic Surface Snow Bacterial Communities
Financement 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.

Les personnes impliquées dans le projet:

Lucie Malard

Méthodes d'échantillonnage

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.

Etendue de l'étude 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.

Description des étapes de la méthode:

  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).

Citations bibliographiques

  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

Métadonnées additionnelles