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Airborne Bacteria from Miers Valley, Antarctica

Dernière version Publié par SCAR - Microbial Antarctic Resource System le 19 mars 2019 SCAR - Microbial Antarctic Resource System
Date de publication:
19 mars 2019
Licence:
CC-BY 4.0

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Description

Amplicon dataset of bacteria captured 1 m above the ground in two locations in Miers Valley (Antarctica).

Versions

Le tableau ci-dessous n'affiche que les versions publiées de la ressource accessibles publiquement.

Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Bottos E, Woo A, Zawar-Reza P, Pointing S, Cary C (2018): Airborne Bacteria from Miers Valley, Antarctica. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=airborne_bacteria_miers_antarctica&v=1.2

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 : 6a1177d0-ce25-4611-9666-a3d58cdea8c5.  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:
-

Eric Bottos
University of Waikato
Hamilton
NZ
Antony Woo
Sorbonne Paris Cité
Paris
FR
Peyman Zawar-Reza
University of Waikato
Hamilton
NZ
Stephen Pointing
University of Waikato
Hamilton
NZ
Craig Cary
University of Waikato
Hamilton
NZ

Personne pouvant répondre aux questions sur la ressource:

Stephen Pointing
University of Waikato
Hamilton
NZ

Personne ayant renseigné les métadonnées:
-

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Natural Sciences
Brussels
BE

Autres personnes associées à la ressource:

Couverture géographique

Miers Valley, Antarctica

Enveloppe géographique Sud Ouest [-78,114, 163,786], Nord Est [-78,096, 163,787]

Couverture taxonomique

16S ssu rRNA

Domain Bacteria (Bacteria)

Couverture temporelle

Epoque de formation 2009-12-11 2010-01-25

Méthodes d'échantillonnage

Aerosol samples were collected by filtration onto 0.2-μm-pore-size polycarbonate filters by impaction using solar-powered pumps (SKC, 224-PCXR8, Eighty Four, PA, USA) mounted 1 m above the ground in each location. Filters inserted into cassette apparatus but not exposed to air flow were used as controls. All filters and cassettes were UV-sterilized and rinsed with 70 % alcohol before use. Sampling apparatus was deployed 1 m above the ground surrounded with a 2 mm gauze baffle on the Miers Valley Floor (78°05′.78S, 163°47′.25E, approx. 270 m) and Miers Valley Ridge (78°06′.83S, 163°47′.18E, approx. 550 m).

Etendue de l'étude Samples were collected from a continuous filtration period December 11, 2009 to January 25, 2010 (55 days), with an estimated sample volume of 75,000 l for each location.

Description des étapes de la méthode:

  1. Air sampling (see sampling description)
  2. Filters were stored at −20 °C during transit from Antarctica and until processed.
  3. Total DNA was extracted directly from the filters using the DNeasy Plant Mini Kit (Qiagen, CA, USA), after first washing with kit lysis buffer for 10 min. The remaining steps of the extraction were carried out according to the manufacturers instructions. Recovered DNA was quantified using NanoDrop™ (Thermo Scientific, Waltham, MA, USA).
  4. For each sample, PCR targeting the V5–V7 region of the 16S rRNA gene was completed in duplicate. Each 30 μl reaction contained 1× PrimeSTAR buffer, 0.2 mM dNTPs, 0.75 U PrimeSTAR HS DNA Polymerase (Takara Holdings, Kyoto, Japan), 0.4 μM of primers Tx9 (5′-GGATTAGAWACCCBGGTAGTC-3′) and 1391R (5′-GACGGGCRGTGWGTRCA-3′), and 5 μl of template DNA. Thermal cycling conditions consisted of 94 °C for 3 min; 30 cycles of 94 °C for 20 s, 52 °C for 20 s, and 72 °C for 45 s; and 72 °C for 3 min. All thermal cycling was completed on a Bio-Rad DNA Engine Peltier Thermal Cycler 200 (Bio-Rad, Hercules, CA, USA). Duplicate reactions were pooled, and amplicons were size-selected from agarose gels using a MO BIO Gel Extraction Kit (MO BIO Laboratories, Carlsbad, CA, USA). Gel extracted products were cleaned using an Agencourt AMPure XP system (Beckman Coulter, Brea, CA, USA) and quantified using a Qubit dsDNA HS Assay Kit and Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA).
  5. To prepare the amplicons for sequencing, a second round of PCR was completed in triplicate. PCR reactions were prepared as outlined above, but using 10 ng of purified amplicon as the template and primers MIDX-Tx9F (5′-CCATCTCATCCCTGCGTGTCTCCGACTCAG-MID-GGATTAGAWACCCBGGTAGTC-3′) and BacB_1391R (5′-CCTATCCCCTGTGTGCCTTGGCAGTCTCAG-GACGGGCRGTGWGTRCA-3′), adapted for one-way reads with unique MID identifiers for each sample. Thermal cycling conditions were as outlined above, but reduced to 13 cycles. Triplicate products were pooled, gel-extracted, cleaned, and quantified as outlined above, before quantification of amplifiable molecules using a KAPA Library Quantification Kit for Roche 454 Titanium/Universal (Kapa Biosystems, Woburn, MA, USA) on a Corbett Rotor-Gene 6000 real-time thermal cycler (Life Technologies). Amplicons were sequenced using the GS Junior Titanium emPCR Kit (Lib-L), the GS Junior Titanium Sequencing Kit, PicoTitrePlate Kit, and GS Junior System (Roche 454 Life Sciences, Branford, CT, USA) at The University of Waikato DNA Sequencing Facility.

Citations bibliographiques

  1. Bottos, E. M., Woo, A. C., Zawar-Reza, P., Pointing, S. B., & Cary, S. C. (2014). Airborne bacterial populations above desert soils of the McMurdo Dry Valleys, Antarctica. Microbial ecology, 67(1), 120-128.

Métadonnées additionnelles

Identifiants alternatifs 6a1177d0-ce25-4611-9666-a3d58cdea8c5
https://ipt.biodiversity.aq/resource?r=airborne_bacteria_miers_antarctica