Microbial fungal communities (18S) of Antarctic Dry Valley lakes

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 fungi (18S ssu rRNA gene, v7-v8) in Antarctic Dry Vallei lakes.

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¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

Rojas-Jimenez K, Wurzbacher C, Bourne E C, Chiuchiolo A, Priscu J, Grossart H (2018): Microbial fungal communities (18S) of Antarctic Dry Valley lakes. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=fungal_communities_of_antarctic_dry_valley_lakes&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: 69245174-bc73-48cc-ae36-3bbbd27c237b.  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?:

Keilor Rojas-Jimenez
eibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin DE
Christian Wurzbacher
Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin DE
Elizabeth Charlotte Bourne
eibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin DE
Amy Chiuchiolo
Research associate
Montana State University Bozeman US
John Priscu
Montana State University Bozeman US
Hans-Peter Grossart
eibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin DE

¿Quién puede resolver dudas acerca del recurso?:

Keilor Rojas-Jimenez
eibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin DE

¿Quién documentó los metadatos?:

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

¿Quién más está asociado con el recurso?:

Usuario

Cobertura Geográfica

Lakes in the McMurdo Dry Valleys, Antarctica

Coordenadas límite Latitud Mínima Longitud Mínima [-78.1, 162.367], Latitud Máxima Longitud Máxima [-77.617, 166.667]

Cobertura Taxonómica

Fungi, 18S ssu rRNA marker gene

Dominio  Fungi (Fungi)

Datos del Proyecto

No hay descripción disponible

Título Microbial fungal communities (18S) of Antarctic Dry Valley lakes
Fuentes de Financiación Funding was provided by the Leibniz “Mycolink” SAW project (Pakt/SAW-2014-IGB-1) given to HPG and ECB. JCP was funded by US National Science Foundation grants PLR1439774, PLR1115245, PLR 1543537 and NASA NRA NNH14ZDA001N-PSTAR.

Personas asociadas al proyecto:

Keilor Rojas-Jimenez

Métodos de Muestreo

Water samples (1–2 l) were collected at selected depths through a ~30 cm diameter borehole in the ca. 4 m thick ice covers of each lake using sterile Niskin bottles. To prevent the introduction of contaminants into the lakes, precautions were taken to drill just to the surface of the water. Prior to use, each corer was rinsed properly. For each lake a different sampler was used to avoid cross contamination. In addition, we established a suitable waiting period between the drilling and the water sampling. Then, the samples were filtered through 5.0 µm Puradisc Cellulose Nitrate syringe filters (Gelman Sciences, USA) and subsequently through 0.2 µm Sterivex filters (Millipore, USA) to distinguish between particle-associated and small free-living eukaryotes. Filters were stored with 2.0 ml of Puregene lysis buffer at −80 °C until further processing and nucleic acid extraction.

Área de Estudio Samples were taken during the austral summers of 2011–2012 from five lake basins in the Taylor and Miers Valleys that are the focus of the McMurdo Dry Valleys Long-Term Ecological Research program (MCM LTER).

Descripción de la metodología paso a paso:

  1. DNA from the microorganisms in the filters was extracted using a phenol-chloroform protocol. From 12 samples of the West and East lobes of Lake Bonney, we also extracted RNA using an RNeasy Mini Kit (QIAGEN, Germany). The RNA was converted to cDNA with a One-Step RT-PCR Kit (QIAGEN, Germany) according to the manufacturer’s instructions. We amplified the V7 and V8 regions of the 18S rRNA gene using primers FF390 (5′-CGATAACGAACGAGACCT-3′) and FR1 (5′-AICCATTCAATCGGTAIT-3′).
  2. For the 25 µl PCR reaction, we used a proof reading enzyme (Herculase II Fusion Polymerase, Agilent Technologies, Santa Clara, USA) and 40 ng DNA (or cDNA) as a template with the following conditions; 95 °C for 3 min initial denaturation followed by 35 cycles at 95 °C for 45 s, 52 °C for 1 min, 72 °C for 1 min, and a final extension at 72 °C for 5 min. The 96 resulting amplicons (~350 bp) went into the library preparation for Illumina MiSeq sequencing according to the protocol presented by the Illumina customer letter for 16 S sequencing with custom primers (Illumina guide to 16 S amplicon sequencing, Part # 15044223 Rev. A) and the Nextera index kit (Illumina, San Diego, USA). The samples were sequenced on a MiSeq sequencer (Illumina, San Diego, USA) with v3 2 × 300 nt chemistry. Sequences were demultiplexed with flexbar resulting in 6.4 M sequences.

Referencias Bibliográficas

  1. Rojas-Jimenez, K., Wurzbacher, C., Bourne, E. C., Chiuchiolo, A., Priscu, J. C., & Grossart, H. P. (2017). Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica. Scientific reports, 7(1), 15348.

Metadatos Adicionales

Identificadores Alternativos 69245174-bc73-48cc-ae36-3bbbd27c237b
https://ipt.biodiversity.aq/resource?r=fungal_communities_of_antarctic_dry_valley_lakes