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

Versão mais recente published by SCAR - Microbial Antarctic Resource System on mar 19, 2019 SCAR - Microbial Antarctic Resource System
Publication date:
19 de Março de 2019
Licença:
CC-BY 4.0

Baixe a versão mais recente dos metadados como EML ou RTF:

Metadados como um arquivo EML download em English (11 KB)
Metadados como um arquivo RTF download em English (13 KB)

Descrição

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)

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

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

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: 53b30953-201f-4599-9377-1c41b5cba477.  SCAR - Microbial Antarctic Resource System publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por Scientific Committee on Antarctic Research.

Palavras-chave

Metadata

Contatos

Craig Herbold
  • Originador
  • Ponto De Contato
The University of Waikato
Hamilton
NZ
Charles Lee
  • Originador
The University of Waikato
Hamilton
NZ
Ian McDonald
  • Originador
The University of Waikato
Hamilton
NZ
Craig Cary
  • Originador
The University of Waikato
Hamilton
NZ
Maxime Sweetlove
  • Provedor Dos Metadados
Research assistent
Royal Belgian Institite for Natural Sciences
Rue Vautier 29
1000 Brussels

Cobertura Geográfica

Tramway Ridge (ASPA 130), Mount Erebus, Antarctica

Coordenadas delimitadoras Sul Oeste [-77,518, 167,111], Norte Leste [-77,518, 167,111]

Cobertura Taxonômica

metagenomic data (amplicon and shotgun) of Bacteria

Domínio Bacteria (Bacteria)

Dados Sobre o Projeto

Nenhuma descrição disponível

Título Evidence of global-scale aeolian dispersal and endemism in isolated geothermal microbial communities of Antarctica
Financiamento 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).

O pessoal envolvido no projeto:

Craig Herbold

Métodos de Amostragem

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.

Área de Estudo 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).

Descrição dos passos do método:

  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.

Citações bibliográficas

  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.

Metadados Adicionais

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