メタデータ

Surface and deep marine bacterial communities in the Arctic and Antarctic

最新バージョン SCAR - Microbial Antarctic Resource System によって公開 2019/03/19 SCAR - Microbial Antarctic Resource System

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説明

Amplicon sequencing dataset (454 pyrosequencing) of Bacteria (16S ssu rRNA gene, v6 region) in surface and deep waters of the Arctic and the Southern oceans. This dataset is part of the International Census of Marine Microbes (ICoMM).

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。:

Ghiglione J, Galand P, Pommier T, Pedros-Alio C, Maas E, Bakker K, Bertilson S, Kirchman D, Lovejoy C, Yager P, Murray A (2019): Surface and deep marine bacterial communities in the Arctic and Antarctic. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=pole_to_pole_marine_bacterial_communities&v=1.1

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: 8d3fae22-72bd-4e8f-adcd-7f57079c87ce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:
-

Jean-François Ghiglione
University Pierre et Marie Curie
FR
Pierre Galand
University Pierre et Marie Curie
FR
Thomas Pommier
Institut National de la Recherche Agronomique (INRA)
Villeurbanne
FR
Carlos Pedros-Alio
Institut de Ciències del Mar
Barcelona
ES
Elizabeth Maas
National Institute of Water and Atmospheric Research
Wellington
NZ
Kevin Bakker
University of Georgia
Athens
US
Stefan Bertilson
Uppsala University
Uppsala
SE
David Kirchman
University of Delaware
Lewes
US
Connie Lovejoy
Université Laval
Québec
CA
Patricia Yager
University of Georgia
Athens
US
Alison Murray
Desert Research Institute
Reno
US

リソースに関する質問に答えることができる人:

Jean-François Ghiglione
University Pierre et Marie Curie
FR
Alison Murray
Desert Research Institute
Reno
US

メタデータを記載した人:
-

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

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

The Arctic Ocean and the Southern Ocean

座標(緯度経度) 南 西 [-73.96, -159.34], 北 東 [79.99, 126]

生物分類学的範囲

Bacteria (16S ssu rRNA gene, v6 region)

Domain Bacteria (Bacteria)

プロジェクトデータ

The role of the International Census of Marine Microbes (ICoMM) is to promote an agenda and an environment that will accelerate discovery, understanding, and awareness of the global significance of marine microbes. More details can be found in: Amaral-Zettler, L., Artigas, L.F., Baross, J., Bharathi, L., Boetius, A., Chandramohan, D., Herndl, G., Kogure, K., Neal, P., Pedros-Alio, C., Ramette, A., Schouten, S., Stal, L., Thessen, A., de Leeuw, J. & Sogin, M. 2010. A global census of marine microbes, In: Life in the World's Oceans: Diversity, Distribution and Abundance, Blackwell Publishing Ltd., Oxford, (Ed. McIntyre), pp. 223-45.

タイトル International Census of Marine Microbes
識別子 ICoMM
ファンデイング Funding to support sample collection was provided by the Institut Français pour la Recherche et la Technologie Polaires; the Spanish Ministry of Education and Science; the New Zealand International Polar Year-Census of Antarctic Marine Life Project [Phases 1 (So001IPY) and 2 (IPY2007-01)); the Natural Sciences and Engineering Council (NSERC) of Canada; National Science Foundation Grants OPP-0124733, ANT-0632389, and ANT-0741409; and the Swedish Polar Research Secretariat. Pyrosequencing was provided by the International Census of Marine Microbes (ICoMM) with financial support from a W. M. Keck Foundation award to the Marine Biological Laboratory in Woods Hole.

プロジェクトに携わる要員:

Linda Amaral-Zettler

収集方法

Samples were collected with a 5 l Niskin bottle.

Study Extent Water samples were taken from the Southern and the Arctic Oceans

Method step description:

  1. DNA extraction buffer (0.1 M Tris-HCl [pH 8], 0.1 M Na-EDTA [pH 8], 0.1 M NaH2PO4 [pH 8], 1.5 M NaCl, 5% cetyltri- methylammonium bromide), and proteinase K (1%) was added to each filter. Samples were frozen at -80°C and thawed at 65°C three times and then incubated on a rotating carousel for 30 min at 37°C. Sodium dodecyl sulfate (SDS; 20%) was added to each sample, and the samples were incubated at 65°C on a rotating carousel for 2 h. The liquid was then removed from the filters using a 3-ml syringe and placed in a 2-ml microcentrifuge tube, which was centrifuged at room temperature (6,000 g; 5 min). The supernatant from each microcentrifuge tube was then placed in separate 15-ml Falcon collection tubes. DNA extraction buffer, lysozyme (200 ul; 50 mg ml), SDS, and proteinase K were then added to each filter (1 ml and 75 and 20 ul, respectively) and to each microcentrifuge tube containing spun-down particles (0.37 ml and 75 and 10 ul, respectively). Both the filter samples and the microcentrifuge tubes were incubated on a rotating carousel for 10 min. The microcentrifuge tubes were again centrifuged (6,000 g; 5 min), and the supernatant was added to the appropriate collection tube. Liquid was then removed from the filters, placed in the microcentrifuge tubes, and centrifuged (6,000 g; 5 min), and the supernatant was added to the collection tubes. The extraction buffer, SDS, and proteinase K were added to each filter and the particles again, and the extraction process was repeated. An equal volume of phenol:chloroform:isoamyl alcohol step (25:24:1) was added to each collection tube of supernatant, and the tubes were vortexed and centri- fuged (1,200 g; 10 min). The aqueous (top) layer from each tube was drawn off into a 30-ml acid-washed sterile Corex (Corning) tube, and an equal volume of isopropanol was added to each tube and mixed gently. Often additional aliquots of isopropanol-water (1:1) were added to adequately dissolve the aqueous layer in the isopropanol. After the tubes were incubated for 1 h at room temperature, the precipitated DNA was centrifuged at room temperature (16,000 g; 20 min), and the isopropanol supernatant was removed and replaced with 5 ml of 70% ethanol. After a final centrifugation (16,000 g; 20 min), the ethanol was removed and the DNA was dried down and resuspended in 95 ul of TE buffer (10 mM Tris 1 mM EDTA, pH 8.0). The DNA was purified using Qiaquick PCR purification columns (Qiagen) according to the manufacturer’s instructions and stored at 20°C.
  2. PCR amplicon was done by adding genomic DNA (3–10 ng) to three separate 30 ul amplification mixes. The amplification mix contained 5 units of Pfu Turbo polymerase (Stratagene, La Jolla, CA), 1 Pfu reaction buffer, 200 uM dNTPs (Pierce Nucleic Acid Technologies, Milwaukee, WI), and a 0.2 uM concentration of each primer in a volume of 100 ul. Cycling conditions were an initial denaturation at 94°C for 3 min; 30 cycles of 94°C 30 s, 57°C for 45 s, and 72°C for 1 min; and a final 2-min extension at 72°C. The products were pooled after cycling and cleaned by using the MinElute PCR purification kit (Qiagen, Valencia, CA). The quality of the product was assessed on a Bioanalyzer 2100 (Agilent, Palo Alto, CA) using a DNA1000 LabChip. Only sharp, distinct amplification products with a total yield of 200 ng were used for 454 sequencing. The fragments in the amplicon libraries were bound to beads under conditions that favor one fragment per bead. The beads were emulsified in a PCR mixture in oil, and PCR amplification occurred in each droplet, generating 10 million copies of a unique DNA template. After breaking the emulsion, the DNA strands were denatured, and beads carrying single- stranded DNA clones were deposited into wells on a PicoTiter- Plate (454 Life Sciences) for pyrosequencing on a Genome Sequencer 20 system (Roche, Basel, Switzerland).

書誌情報の引用

  1. Amaral-Zettler, L., Artigas, L.F., Baross, J., Bharathi, L., Boetius, A., Chandramohan, D., Herndl, G., Kogure, K., Neal, P., Pedros-Alio, C., Ramette, A., Schouten, S., Stal, L., Thessen, A., de Leeuw, J. & Sogin, M. 2010. A global census of marine microbes, In: Life in the World's Oceans: Diversity, Distribution and Abundance, Blackwell Publishing Ltd., Oxford, (Ed. McIntyre), pp. 223-45.
  2. Ghiglione, J. F., Galand, P. E., Pommier, T., Pedrós-Alió, C., Maas, E. W., Bakker, K., ... & Murray, A. E. (2012). Pole-to-pole biogeography of surface and deep marine bacterial communities. Proceedings of the National Academy of Sciences, 201208160.

追加のメタデータ

代替識別子 8d3fae22-72bd-4e8f-adcd-7f57079c87ce
https://ipt.biodiversity.aq/resource?r=pole_to_pole_marine_bacterial_communities