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

Última versión Publicado por SCAR - Microbial Antarctic Resource System en 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

Descargas

Descargue la última versión de los metadatos como EML o RTF:

Metadatos como un archivo EML descargar en Inglés (10 KB)
Metadatos como un archivo RTF descargar en Inglés (9 KB)

Versiones

La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.

¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: 3a0fa23f-411a-49ec-96ed-3ee8cf7d5696.  SCAR - Microbial Antarctic Resource System publica este recurso, y está registrado en GBIF como un publicador de datos avalado por Scientific Committee on Antarctic Research.

Palabras Clave

Metadata

Contactos

¿Quién creó el recurso?:

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

¿Quién puede resolver dudas acerca del recurso?:

Deric Learman
Central Michigan University Mt. Pleasant US

¿Quién documentó los metadatos?:

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

¿Quién más está asociado con el recurso?:

Usuario

Cobertura Geográfica

Southern Ocean marine sediment samples (Antarctica)

Coordenadas límite Latitud Mínima Longitud Mínima [-76.55, -102.159], Latitud Máxima Longitud Máxima [-62.535, 170]

Cobertura Taxonómica

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

Dominio  Bacteria (Bacteria),  Archaea (Archaea)

Eukaryotes (18S ssu rRNA gene, v4 region)

Dominio  Eukaryota (Eukaryotes)

Cobertura Temporal

Fecha Inicial 2014-01-01

Datos del Proyecto

No hay descripción disponible

Título Microbes (16S and 18S rRNA genes) from benthic Antarctic sediments
Fuentes de Financiación 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.

Personas asociadas al proyecto:

Deric Learman

Métodos de Muestreo

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.

Área de Estudio 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.

Descripción de la metodología paso a paso:

  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.

Referencias Bibliográficas

  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.

Metadatos Adicionales

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