Microbes (16S and 18S rRNA genes) from benthic Antarctic sediments

Dernière version Publié par SCAR - Microbial Antarctic Resource System le Mar 19, 2019 SCAR - Microbial Antarctic Resource System

amplicon sequencing dataset (Illumina MiSeq) of microbial communities (16S and 18S rRNA genes) in 24 samples from benthic Antarctic sediments

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Learman D, Henson M, Thrash C, Temperton B, Brannock P, Santos S, Mahon A, Halanych K (2019): Microbes (16S and 18S rRNA genes) from benthic Antarctic sediments. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbes_in_benthic_antarctic_sediments&v=1.2

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. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 3a0fa23f-411a-49ec-96ed-3ee8cf7d5696.  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:

Deric Learman
Central Michigan University Mt. Pleasant US
Michael Henson
Louisiana State University Baton Rouge US
Cameron Thrash
Louisiana State University Baton Rouge US
Ben Temperton
University of Exeter Exeter GB
Pamela Brannock
Auburn University Auburn US
Scott Santos
Auburn University Auburn US
Andrew Mahon
Central Michigan University Mt. Pleasant US
Kenneth Halanych
Auburn University Auburn US

Personne pouvant répondre aux questions sur la ressource:

Deric Learman
Central Michigan University Mt. Pleasant US

Personne ayant renseigné les métadonnées:

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

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

Southern Ocean marine sediment samples (Antarctica)

Enveloppe géographique Sud Ouest [-76.55, -102.159], Nord Est [-62.535, 170]

Couverture taxonomique

Bacteria and Archaea (16S ssu rRNA gene, v4 region)

Domain  Bacteria (Bacteria),  Archaea (Archaea)

Eukaryotes (18S ssu rRNA gene, v4 region)

Domain  Eukaryota (Eukaryotes)

Couverture temporelle

Date de début 2014-01-01

Données sur le projet

Pas de description disponible

Titre Microbes (16S and 18S rRNA genes) from benthic Antarctic sediments
Financement Funds through NSF Antarctic Program: Award Number 1043670 and 1043745, and from Central Michigan University Faculty Research and Creative Endeavors Committee and College of Science and Technology.

Les personnes impliquées dans le projet:

Deric Learman

Méthodes d'échantillonnage

Samples were collected on the Antarctic shelf at depths ranging from 223 to 820 m. The top 3 cm of sediments were transferred into sampling tubes and stored frozen (−80°C). Samples were shipped frozen to Central Michigan University within 3 months of collection.

Etendue de l'étude Surface sediment samples were collected from the continental shelf of Antarctica during two research cruises. The first cruise (Dec. 2013–Feb. 2014, RVIB Nathaniel B. Palmer) sampled Western Antarctica, which includes the Amundsen Sea, Bellingshausen Sea, and Ross Sea, using a multicorer. The second cruise (Nov.–Dec. 2014, ASRV Laurence M. Gould) sampled the Antarctic Peninsula using a box corer.

Description des étapes de la méthode:

  1. DNA was extracted using a PowerSoil DNA extraction kit (MoBio) following the manufacturer's protocol. Approximately 4–8 extractions were completed on each sediment sample and pooled and concentrated with a DNA Clean and Concentrator kit (Zymo) due to low yields from some of the samples. DNA was then quantified using the Qubit2.0 Fluorometer (Life Technologies) and stored at −20°C. Bacterial and archaeal sequences were generated from the V4 region of 16S rRNA gene using the primer set 515f and 806r while eukaryotic sequences were obtained with the V4 region of the 18S rRNA gene using the primer set 1391r and EukBR. Resulting amplicons were sequenced on an Illumina MiSeq as paired-end (PE) reads of 250-bp at Michigan State University's (MSU) Research Technology Support Facility (RTSF) Genomics Core.

Citations bibliographiques

  1. Learman, D. R., Henson, M. W., Thrash, J. C., Temperton, B., Brannock, P. M., Santos, S. R., ... & Halanych, K. M. (2016). Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure. Frontiers in microbiology, 7, 284.

Métadonnées additionnelles

Identifiants alternatifs 3a0fa23f-411a-49ec-96ed-3ee8cf7d5696
https://ipt.biodiversity.aq/resource?r=microbes_in_benthic_antarctic_sediments