Marine_ microbial eukaryotes (18S) from the Ross Sea (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

Amplicon sequencing dataset of microbial eukaryotes (18S ssh rRNA gene v9) in water and sea ice collected in the Ross Sea, Antarctica during the summer of 2011. Prior to sequencing, mixotroph abundances were determined using tracer ingestion.

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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。:

Gast R, Fay S, Sanders R (2018): Marine_ microbial eukaryotes (18S) from the Ross Sea (Antarctica). v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=marine_microbial_eukaryotes_18s_experiment_rosssea&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: b9c72483-b00a-4848-9239-b36dce06b0cb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:

Rebecca Gast
Woods Hole Oceanographic Institution Woods Hole US
Scott Fay
Temple University Philadelphia US
Robert Sanders
Temple University Phyladelphia US

リソースに関する質問に答えることができる人:

Rebecca Gast
Woods Hole Oceanographic Institution Woods Hole US

メタデータを記載した人:

Maxime Sweetlove
rResearch assistent
Royal Belgian Institute 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

Southern Ocean: Ross Sea, Antarctica

座標(緯度経度) 南 西 [-75.44, -171.29], 北 東 [-72.35, 178.3]

生物分類学的範囲

Microbial eukaryotes (18S ssh rRNA gene, v9 region)

Domain  Eukaryote (Eukaryotes)

時間的範囲

開始日 / 終了日 2011-01-26 / 2011-02-08

プロジェクトデータ

説明がありません

タイトル National Science Foundation Grants OPP-0838955 (RG) and OPP-0838847 (RS)
ファンデイング This work was supported by National Science Foundation Grants OPP-0838955 (RG) and OPP-0838847 (RS).

プロジェクトに携わる要員:

Rebecca Gast

収集方法

Seawater was collected from two depths (surface and deep chlorophyll maximum) at 10 open water stations using 30 liter Niskin bottles on a CTD rosette. Two of those sites were sampled a second time on different dates. The deep chlorophyll maximum (CM) was determined by fluorescence (WetLabs FLRTD fluorometer) during the downcast of the CTD and ranged from 30 to 90 m in depth depending on station.

Study Extent Samples for shipboard experiments were collected in the Ross Sea during research cruise NBP-1101 aboard the R/V Nathaniel B. Palmer in the austral summer (20 January through 13 February 2011).

Method step description:

  1. A strain of bacteria, Planococcus sp., with a diameter < 1 μm was labeled with BrdU (5′-bromo-2′-deoxyuridine, Sigma B5002) by inoculating into 50 mL of fresh media (1% yeast extract, 0.22 μm filtered seawater) with 20 μM BrdU. Planococcus for control incubations was treated identically except that BrdU was excluded from the media. The bacterial cells were harvested by centrifugation (3,000 × g, 10 min), washed 3 times, and dispersed and resuspended by pipetting with cold phosphate-buffered saline.
  2. There were two treatments per experiment; the addition of BrdU-labeled Planococcus and the addition of unlabeled Planococcus. Planococcus was added at 10% of the natural abundance of bacteria for the first experiment and at 20% for the remaining three BrdU incubation experiments. All cubitainers were incubated at −0.5°C in continuous fluorescent light at ~7 × 1015 quanta s−1 cm−2 (surface samples) and ~7 × 1014 quanta s−1 cm−2 (CM samples). Samples (1–2 L) were taken after 72 h of incubation for each depth/replicate, collected on 0.2 μm Durapore filters and frozen at −80°C for later extraction.
  3. DNA was extracted following the protocol in Gast et al. (2004), resuspended in 100 μL 1 × Tris/EDTA and stored frozen at −80°C for transport. Immunoprecipitation of BrdU-labeled DNA was performed following the protocol modified and published by Fay et al. (2013). Samples of DNA from incubations that were fed unlabeled bacteria are identified as “Whole,” whereas the samples fed BrdU-labeled bacteria are identified as “IP” (immunoprecipitated).
  4. Primers to amplify the V9 region of the 18S ribosomal RNA gene were used to generate products for amplicon high throughput sequencing. For each sample, 3 PCR reactions were performed at a volume of 50 μl each that contained 0.2 μM of each primer, 1× reaction buffer, 200 μM each dNTP, and 0.5U Phusion DNA Polymerase (New England Biolabs F-553). Cycling conditions were: 98°C for 120 s; 10 cycles of 98°C for 15 s, 67°C decreased by 1°C cycle−1 for 20 s, and 72°C for 15 s; 25 cycles of 98°C for 15 s, 57°C for 20 s, and 72°C for 15 s; and a final extension step of 72°C for 120 s. Each sample was purified with AMPure XP beads (Beckman Coulter A63880) following the manufacturer's protocol.
  5. Sequencing was accomplished on pooled triplicate samples at the University of Pennsylvania DNA Sequencing Facility using a “1-way read” approach for amplicon pyrosequencing with the GS Junior emPCR Lib-L kit (454 Life Sciences) on a Roche/454 GS-FLX.

書誌情報の引用

  1. Gast, R. J., Fay, S. A., & Sanders, R. W. (2018). Mixotrophic Activity and Diversity of Antarctic Marine Protists in Austral Summer. Frontiers in Marine Science, 5, 13.

追加のメタデータ

代替識別子 b9c72483-b00a-4848-9239-b36dce06b0cb
https://ipt.biodiversity.aq/resource?r=marine_microbial_eukaryotes_18s_experiment_rosssea