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

Dernière version Publié par SCAR - Microbial Antarctic Resource System le 9 juin 2021 SCAR - Microbial Antarctic Resource System
Date de publication:
9 juin 2021
Licence:
CC-BY 4.0

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Description

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.

Versions

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

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

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 5b2d711b-85ba-4219-8368-c3c3b2236bd4.  SCAR - Microbial Antarctic Resource System publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Scientific Committee on Antarctic Research.

Mots-clé

Metadata

Contacts

Personne ayant créé cette ressource:
-

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

Personne pouvant répondre aux questions sur la ressource:

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

Personne ayant renseigné les métadonnées:
-

Maxime Sweetlove
Royal Belgian Institute of Natural Sciences
Brussels
BE

Autres personnes associées à la ressource:

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

Couverture géographique

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

Enveloppe géographique Sud Ouest [-65,613, -66,441], Nord Est [-64,815, -62,593]

Couverture temporelle

Date de début / Date de fin 2014-12-10 / 2014-12-23

Données sur le projet

Pas de description disponible

Titre Seasonal Trophic Roles of Euphausia superba (STRES) project
Financement 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.
Description du domaine d'étude / de recherche Southern Ocean around the Antarctic Peninsula

Les personnes impliquées dans le projet:

Alison Cleary

Méthodes d'échantillonnage

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.

Etendue de l'étude Euphausia superba specimen were collected during the cruise NBP1410 of the US RV Ice Breaker ‘Nathaniel B. Palmer’ between 10 and 21 December 2014.
Contrôle qualité 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.

Description des étapes de la méthode:

  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.

Citations bibliographiques

  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.

Métadonnées additionnelles