fumarolic microbial communities at Tramway Ridge, Mt. Erebus, Antarctica

Dernière version Publié par SCAR - Microbial Antarctic Resource System le Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Microbial (Bacteria) Dataset containing amplicon sequencing samples and metagenome shotgun sequencing samples from two fumarole soil location at Tramway Ridge, Mount Erebus, Antarctica (ASPA 130)

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Herbold C, Lee C, McDonald I, Cary C (2019): fumarolic microbial communities at Tramway Ridge, Mt. Erebus, Antarctica. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=fumarolic_antarctic_microbial_communities_at_mount_erebus&v=1.2

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L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

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Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 53b30953-201f-4599-9377-1c41b5cba477.  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:

Craig Herbold
The University of Waikato Hamilton NZ
Charles Lee
The University of Waikato Hamilton NZ
Ian McDonald
The University of Waikato Hamilton NZ
Craig Cary
The University of Waikato Hamilton NZ

Personne pouvant répondre aux questions sur la ressource:

Craig Herbold
The University of Waikato Hamilton NZ

Personne ayant renseigné les métadonnées:

Maxime Sweetlove
Research assistent
Royal Belgian Institite for Natural Sciences Rue Vautier 29 1000 Brussels

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

Tramway Ridge (ASPA 130), Mount Erebus, Antarctica

Enveloppe géographique Sud Ouest [-77.518, 167.111], Nord Est [-77.518, 167.111]

Couverture taxonomique

metagenomic data (amplicon and shotgun) of Bacteria

Domain  Bacteria (Bacteria)

Données sur le projet

Pas de description disponible

Titre Evidence of global-scale aeolian dispersal and endemism in isolated geothermal microbial communities of Antarctica
Financement Financial support was provided by grant UOW0802 from the New Zealand Marsden Fund. Additional salary support was provided by the New Zealand Marsden fund to C.K.L. (UOW1003) and C.W.H. (UOW0802).

Les personnes impliquées dans le projet:

Craig Herbold

Méthodes d'échantillonnage

All suggested sterilization protocols for entering into this protected site were adhered to, following the ASPA 130 Management Plan ( http://www.scar.org/publications/bulletins/151/aspa130.html). Sites were chosen based on measuring a surface temperature of 65 °C with a stainless steel Checktemp1 temperature probe (Hanna Instruments, Rhode Island, USA), sterilized with 70% ethanol immediately before each use. Surface ‘crust’ was set aside before collecting samples. Samples were collected by aseptically removing the top 2 cm of sediment in an ~25 cm2 area. Sediment was placed into a fresh 50 ml Falcon tube. Sampling continued with the collection of a second (2–4 cm depth) and third (4–8 cm depth) layer following the same procedures. Temperature measurements were repeated for each layer sampled. All samples were immediately frozen, transported back to the University of Waikato frozen and maintained at −80 °C in the laboratory until analysed.

Etendue de l'étude Sediment samples were collected within the Tramway Ridge Antarctic Specially Protected Area (ASPA 130) in February 2009 from two sites (site A (active site): 77° 31.103′ S, 167° 6.682′ S and site B (passive site): 77° 31.106′ S, 167° 6.668′ E).

Description des étapes de la méthode:

  1. DNA was extracted from samples using a modified CTAB (cetyltrimethylammonium bromide) bead-beating protocol. For shotgun sequencing, a portion of extracted genomic DNA was sequenced using standard protocols for the 454-Ti platform (Roche 454 Life Sciences, Branford, CT, USA) at the UCLA GenoSeq CORE.
  2. PCR amplicons containing V5–V7 hypervariable regions of the 16S rRNA gene were generated from the same genomic DNA samples using primers Tx9 (5′-GGATTA GAWACCCBGGTAGTC-3′) and 1391R (5′-GACGGGCRGTGWGTRCA-3′). PCR was performed in triplicate on each sample and pooled to reduce stochastic variation. Three samples (site A 0–2 cm, site B 0–2 cm, site B 2–4 cm) were sequenced using the 454-GS-FLX platform by Taxon Biosciences (Tiburon, CA, USA) and three samples (site A 2–4 cm, site A 4–8 cm and site B 4–8 cm) were sequenced using the 454 Junior platform at the Waikato DNA Sequencing Facility (Hamilton, New Zealand). For the three samples sequenced using the 454-GS-FLX platform, each 30 μl reaction contained 2–10 ng of DNA extract, Pfx polymerase and platinum polymerase (0.5 U each; Invitrogen), 1 × Pfx PCR buffer with Pfx enhancer, 0.2 mM dNTPs, 1 mM MgCl2, 0.02 mg ml−1 BSA, 0.8 μM of forward and reverse primer and PCR-grade water. Thermal cycling conditions were 94 °C for 2 min; 24 cycles of 94 °C for 15 s, 55 °C for 30 s and 68 °C for 1 min; and 68 °C for 3 min. Amplicons were size-selected and purified using polyacrylamide gel electrophoresis before being prepared for pyrosequencing by Taxon Biosciences. For the three samples sequenced using the 454-junior platform, each 30 μl reaction contained 2–10 ng of DNA extract, PrimeStar polymerase (0.625 U; Takara), 1 × PCR buffer, 0.2 mM dNTPs, 0.4 μM of forward and reverse primer and PCR-grade water. Thermal cycling conditions were 94 °C for 3 min; 24 cycles of 94 °C for 20 s, 52 °C for 20 s and 72 °C for 45 s; and 72 °C for 3 min. Triplicate PCR reactions were pooled and gel-purified using the UltraCleanTM 15 DNA Purification Kit (MO BIO Laboratories Inc.), cleaned using the Agencourt AMPure XP Bead Cleanup kit (Beckman Coulter Inc.) and quantified (Quant-iTTM dsDNA HS Assay Kit, Invitrogen Ltd.). Cleaned amplicons were used as template (25 ng) in a second PCR reaction using fusion primers (forward: 5′-(454 Adapter A)-TCAG-MID-Tx9-3′; reverse: 5′-(454 Adapter B)-TCAG-1391R-3′). PCR conditions were exactly the same as the first round except only 10 cycles of PCR were performed. Triplicate PCR reactions were pooled and gel-purified using the UltraCleanTM 15 DNA Purification Kit, cleaned using the Agencourt AMPure XP Bead Cleanup kit and quantified (Quant-iTTM dsDNA HS Assay Kit) before being prepared for pyrosequencing using the 454 Junior platform by the University of Waikato sequencing facility.

Citations bibliographiques

  1. Herbold, C. W., Lee, C. K., McDonald, I. R., & Cary, S. C. (2014). Evidence of global-scale aeolian dispersal and endemism in isolated geothermal microbial communities of Antarctica. Nature communications, 5, 3875.

Métadonnées additionnelles

Identifiants alternatifs 53b30953-201f-4599-9377-1c41b5cba477
https://ipt.biodiversity.aq/resource?r=fumarolic_antarctic_microbial_communities_at_mount_erebus