元數據

Gut content of Antarctic krill Euphausia superba from the West Antarctic Peninsula

最新版本 由 SCAR - Microbial Antarctic Resource System 發佈於 2021年6月9日 SCAR - Microbial Antarctic Resource System
發布日期:
2021年6月9日
授權條款:
CC-BY 4.0

下載最新版本資源元數據的EML或RTF文字檔。

元數據EML檔 下載 在 English 中 (11 KB)
元數據RTF文字檔 下載 在 English 中 (13 KB)

說明

Amplicon sequencing dataset (Illumina MiSeq) targeting Eukaryotes (18S ssu rRNA) in samples (n=186) from seawater or the gut content of Antarctic Krill (Euphausia superba) from the West Antarctic Peninsula.

版本

以下的表格只顯示可公開存取資源的已發布版本。

如何引用

研究者應依照以下指示引用此資源。:

Cleary A, Durbin E, Cacas M (2021): Gut content of Antarctic krill Euphausia superba from the West Antarctic Peninsula. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antarctic_krill_eukaryote_gut_content&v=1.0

權利

研究者應尊重以下權利聲明。:

此資料的發布者及權利單位為 SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF 註冊

此資源已向GBIF註冊,並指定以下之GBIF UUID: 5b2d711b-85ba-4219-8368-c3c3b2236bd4。  SCAR - Microbial Antarctic Resource System 發佈此資源,並經由Scientific Committee on Antarctic Research同意向GBIF註冊成為資料發佈者。

關鍵字

Metadata

聯絡資訊

資源建立者:
-

Alison Cleary
University of Rhode Island Graduate School of Oceanography
Narragansett
US
Edward Durbin
University of Rhode Island Graduate School of Oceanography
Narragansett
US
Maria Cacas
University of Rhode Island Graduate School of Oceanography
Narragansett
US

可回覆此資源相關問題者:

Alison Cleary
University of Rhode Island Graduate School of Oceanography
Narragansett
US

元數據填寫者:
-

Maxime Sweetlove
Royal Belgian Institute of Natural Sciences
Brussels
BE

與此資源的相關者:

Alison Cleary
使用者
University of Rhode Island Graduate School of Oceanography
Narragansett
US

地理涵蓋範圍

Antarctic Peninsula: Adelaide Island, Andvord Bay, Anvers Island, Flandres Bay, Gerlache Strait, Lemaire Strait and Palmer Deep

界定座標範圍 緯度南界 經度西界 [-65.613, -66.441], 緯度北界 經度東界 [-64.815, -62.593]

時間涵蓋範圍

起始日期 / 結束日期 2014-12-10 / 2014-12-23

計畫資料

無相關描述

計畫名稱 Seasonal Trophic Roles of Euphausia superba (STRES) project
經費來源 The STRES project is funded under NSF Office of Polar Programs grant #ANT-1142107. Part of this work was also supported by NSF EPSCoR grant #EPS-1004057.
研究區域描述 Southern Ocean around the Antarctic Peninsula

參與計畫的人員:

Alison Cleary

取樣方法

Krill were collected from the water column with oblique tows of a 1meter squared multiple opening closing net and environmental sensing system (MOCNESS). Net mesh size was 333 μm. Water samples were collected at 10 m depth for DNA analysis of the community composi- tion. Duplicate subsamples of 100 ml of water from each of the sampled areas were filtered onto 0.2 μm pore size, 25 mm diameter membrane filters under gentle vacuum pressure.

研究範圍 Euphausia superba specimen were collected during the cruise NBP1410 of the US RV Ice Breaker ‘Nathaniel B. Palmer’ between 10 and 21 December 2014.
品質控管 Agarose gels with ethidium bromide were used to confirm all sample reactions had produced amplicons of the expected size, and that no amplification was visible in any of the negative controls.

方法步驟描述:

  1. Krill were processed immediately and preserved in 95% reagent grade ethanol. Water filters for DNA analysis were pre- served at −80°C, and were maintained frozen until DNA extraction.
  2. DNA was extracted with the DNeasy blood and tissue kit (Qiagen) as per manufacturer’s directions. Krill stomachs were first broken open with a sterilized toothpick to ensure the contents would fully lyse. For water filters, double volumes were used of lysis buffers to ensure the filter was submerged and thus fully lysed. DNA from krill and water filters were never extracted on the same days.
  3. A nested PCR approach was used to amplify the v7 region from all non-krill 18S rDNA. In the first PCR, krill stomach DNA extracts were amplified with universal 18S primers, while krill’s own DNA was blocked with a krill-specific PNA probe. These reactions included 1× GoTaq Green Master Mix (Promega), 0.5 μM each forward and reverse primers (forward: 5’-GGG CAT CAC AGA CCT G-3’, reverse: 5’-GGC TYA ATT TGA CTC AAC RCG-3’; modified from Gast et al. 2004 as per Cleary et al. 2016), 20 μM krill-specific PNA (from 100 μM stock re-suspended in 2.5% trifluoroacetic acid, 5’-CGT CGG GTT GTC TTG-3’; Cleary et al. 2012), and 20% by volume stomach DNA extract. DNA was used at extracted concentrations. Thermocycling consisted of 95°C for 30 s, followed by 30 cycles of 94°C for 30 s, 67°C for 30 s, 58°C for 30 s, 60°C for 30 s, with a final extension at 60°C for 5 min and then immediate cooling of the reactions to 4°C. In the second PCR, the stomach contents amplicons were re-amplified for only a few cycles with the primers containing the illumina adaptors, in order to add these adaptor sequences onto the ends of the amplicons. These reactions contained 1× GoTaq Green Master Mix, 0.2 μM each forward and reverse primers and 20% by volume amplicons from the first round of PCR
  4. Illumina primers were reversed, which is to say the Read1 adaptor (traditionally forward) was put on the reverse primer, and the Read2 adaptor on the forward primer. Thermocycling for these reactions consisted of 94°C for 30 s, followed by 10 cycles of 94°C for 30 s, 58°C for 30 s, 72°C for 30 s, with a final extension of 72°C for 5 min and then immediate cooling to 4°C.
  5. A final PCR of 5 cycles was performed by the sequencing center to attach further sequencing adaptors and individual tags, and samples were combined into 2 sequencing pools. Krill individuals from each of the sampling locations were divided between the 2 pools; all captive krill were placed in the same pool. Each pool was sequenced in one lane on 2 separate Illumina MiSeq runs, with V2 chemistry for 200 bp in each direction.

引用文獻

  1. Cleary, A. C., Durbin, E. G., & Casas, M. C. (2018). Feeding by Antarctic krill Euphausia superba in the West Antarctic Peninsula: differences between fjords and open waters. Marine Ecology Progress Series, 595, 3
  2. Cleary, A. C., Casas, M. C., Durbin, E. G., & Gómez-Gutiérrez, J. (2019). Parasites in Antarctic krill guts inferred from DNA sequences. Antarctic Science, 31(1), 16-22.