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

Последняя версия опубликована SCAR - Microbial Antarctic Resource System 9 июня 2021 г. SCAR - Microbial Antarctic Resource System
Дата публикации:
9 июня 2021 г.
Лицензия:
CC-BY 4.0

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Описание

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.

Версии

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Как оформить ссылку

Исследователи должны дать ссылку на эту работу следующим образом:

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

Права

Исследователи должны соблюдать следующие права:

Публикующей организацией и владельцем прав на данную работу является SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Регистрация в GBIF

Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: 5b2d711b-85ba-4219-8368-c3c3b2236bd4.  SCAR - Microbial Antarctic Resource System отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке Scientific Committee on Antarctic Research.

Ключевые слова

Metadata

Контакты

Кто является создателем ресурса:
-

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

Кто может ответить на вопросы о ресурсе:

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

Кем заполнены метаданные:
-

Maxime Sweetlove
Royal Belgian Institute of Natural Sciences
Brussels
BE

Кто еще связан с данным ресурсом:

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

Географический охват

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

Ограничивающие координаты Юг Запад [-65,613, -66,441], Север Восток [-64,815, -62,593]

Временной охват

Дата начала / Дата окончания 2014-12-10 / 2014-12-23

Данные проекта

Описание отсутсвует

Название Seasonal Trophic Roles of Euphausia superba (STRES) project
Финансирование 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.
Описание района исследования Southern Ocean around the Antarctic Peninsula

Исполнители проекта:

Alison Cleary

Методы сбора

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.

Охват исследования Euphausia superba specimen were collected during the cruise NBP1410 of the US RV Ice Breaker ‘Nathaniel B. Palmer’ between 10 and 21 December 2014.
Контроль качества 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.

Описание этапа методики:

  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.

Библиографические ссылки

  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.

Дополнительные метаданные

Альтернативные идентификаторы https://ipt.biodiversity.aq/resource?r=antarctic_krill_eukaryote_gut_content