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

最新バージョン SCAR - Microbial Antarctic Resource System によって公開 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)

ダウンロード

メタデータのみリソース のメタデータの最新版をEML または RTF としてダウンロード:

EML ファイルとしてのメタデータ ダウンロード English で (11 KB)
RTF ファイルとしてのメタデータ ダウンロード English で (13 KB)

バージョン

次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。

引用方法

研究者はこの研究内容を以下のように引用する必要があります。:

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

権利

研究者は権利に関する下記ステートメントを尊重する必要があります。:

パブリッシャーとライセンス保持者権利者は SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF登録

このリソースをはGBIF と登録されており GBIF UUID: 53b30953-201f-4599-9377-1c41b5cba477が割り当てられています。   Scientific Committee on Antarctic Research によって承認されたデータ パブリッシャーとして GBIF に登録されているSCAR - Microbial Antarctic Resource System が、このリソースをパブリッシュしました。

キーワード

Metadata

連絡先

リソースを作成した人:

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

リソースに関する質問に答えることができる人:

Craig Herbold
The University of Waikato Hamilton NZ

メタデータを記載した人:

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

他に、リソースに関連付けられていた人:

データ利用者

地理的範囲

Tramway Ridge (ASPA 130), Mount Erebus, Antarctica

座標(緯度経度) 南 西 [-77.518, 167.111], 北 東 [-77.518, 167.111]

生物分類学的範囲

metagenomic data (amplicon and shotgun) of Bacteria

Domain  Bacteria (Bacteria)

プロジェクトデータ

説明がありません

タイトル Evidence of global-scale aeolian dispersal and endemism in isolated geothermal microbial communities of Antarctica
ファンデイング 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).

プロジェクトに携わる要員:

Craig Herbold

収集方法

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.

Study Extent 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).

Method step description:

  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.

書誌情報の引用

  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.

追加のメタデータ

代替識別子 53b30953-201f-4599-9377-1c41b5cba477
https://ipt.biodiversity.aq/resource?r=fumarolic_antarctic_microbial_communities_at_mount_erebus