Community diversity in microbial eukaryotes from lakes in the the Vestfold Hills, Antarctica

Última versión Publicado por SCAR - Microbial Antarctic Resource System en Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (454 pyrosequencing) of microbial eukaryotes (18Sssu rRNA marker gene) in water samples along a salinity gradient (0-250 psu) from the Vestfold Hills, East Antarctica (68°S, 78°E).


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¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

Logares R, Tesson S, Canbäck B, Pontarp M, Hedlund K, Rengefors K (2019): Community diversity in microbial eukaryotes from lakes in the the Vestfold Hills, Antarctica. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata.


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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: 5f4ccd3e-5b1a-4145-aa43-94ecd45ced8a.  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



¿Quién creó el recurso?:

Ramiro Logares
Institute of Marine Sciences Barcelona ES
Sylvie Tesson
Lund University Lund SE
Björn Canbäck
Lund University Lund SE
Mikael Pontarp
Lund University Lund SE
Katarina Hedlund
Lund University Lund SE
Karin Rengefors
Lund University Lund SE

¿Quién puede resolver dudas acerca del recurso?:

Ramiro Logares
Institute of Marine Sciences Barcelona ES

¿Quién documentó los metadatos?:

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

¿Quién más está asociado con el recurso?:


Cobertura Geográfica

Vestfold Hills, East Antarctica The sampled lakes comprise: Lake Abraxas, Ace Lake, Crooked Lake, Deep Lake, Ekho Lake, Lake Hand, Highway Lake, Lebed Lake, Lake McNeil, Organic Lake, Pendant Lake, Rookery Lake, Lake Shield, Vereteno Lake, Lake Watts, and Lake Williams.

Coordenadas límite Latitud Mínima Longitud Mínima [-68.618, 77.917], Latitud Máxima Longitud Máxima [-68.005, 78.414]

Cobertura Taxonómica

Eukaryotes (18S ssu rRNA, v4 region)

Dominio  Eukarya (Eukaryotes)

Cobertura Temporal

Fecha Inicial / Fecha Final 2008-12-29 / 2009-01-29

Datos del Proyecto

The study aims at investigating the protist diversity in 17 aquatic locations in the region of the Vestfold hills, Eastern Antarctica (68°S, 78°E), including one marine site and 16 lakes, across a gradient of salinity spanning from 0 to 250 psu, and over the austral summer period (December 2008-February 2009).

Fuentes de Financiación This project was supported by the Swedish Research Council grants 349-2007-8690 (CAnMove) and 621-2012-3726. Additional support was given by a Ramón y Cajal fellowship (RYC-2013-12554, MINECO, Spain).

Personas asociadas al proyecto:

Ramiro Logares

Métodos de Muestreo

Water samples from different depths were collected in 16 selected lakes as well as in one coastal marine site. Microbes were collected onto polycarbonate filters (Supor-200, 47mm; PALL Corporation, East Hills, NY, USA) and subsequently filters were stored at - 80°C.

Área de Estudio Samples were taken from lakes in the Vestfold Hills (East Antarctica) across a salinity gradient spanning from 0 to 250 psu, and over the austral summer period (December 2008-February 2009).

Descripción de la metodología paso a paso:

  1. Community DNA from each sample was extracted from filter sections using a modified CTAB (Cetyl trimethyl ammonium bromide) extraction protocol in 2mL microfuge tubes along with 0.15g of beads from the PowerSoil™ DNA isolation kit (MOBio, California, USA). Each sample was incubated for 45min at 65°C in a mix of 700μL of CTAB, 24 μL β-mercaptoethanol, and 0.4 mg/mL of RNaseA (Sigma-Aldrich Sweden AB, Stockholm, Sweden), mixing by vortex agitation every 15 min. Samples were then ice-shocked and purified in 700μL of Chloroform:Isoamyl (24:1). After centrifugation (14,000g, 10 min, 4°C), the upper phase was removed and stored at -20°C for 60 min in one volume of isopropanol and a 0.5 volume of NaCl 5M. DNA was then precipitated through two consecutive centrifugations, first at14,000 g and 4°C during 30 min and afterwards, using the same setup during 15 min with 400 μL of ethanol 75%. After removing the supernatant, DNA pellets were dried using a speed vacuum DNA dryer at 300 g, 43°C, during 20 min. Pellets were then dissolved in 40-100 μL of milliQ water. The quality and quantity of DNA was measured using agarose gels (1.5%, TBE 0.5x) as well as a Nanodrop 2000/2000C Spectrophotometer v1.0 (Thermo Scientific, NanoDrop products, Delaware, USA).
  2. Polymerase chain reactions (PCR) were performed in 96 wells plates. For each template DNA, four to nine replicate PCRs were performed following Logares et al. (2012), and subsequently combined. The PCR mix comprised 12.5 μL of 2x Phusion® GC Master Mix (F-532L, Finnzymes Oy, Vantaa, Finland), 4% of DMSO, 10 pmol μL-1 of barcoded fusion primers (Invitrogen™, Life Technologies Europe BV, Stockholm, Sweden), and 5 ng of DNA template in a final volume of 25μL that was adjusted with distilled water. Universal primers adapted from Stoeck et al. (2010) were used to amplify fragments of about 380bp from the V4 18S rDNA region and subsequently sequenced using 454 pyrosequencing. Primers included adapters for uni-directional (library Lib-L) sequencing. The forward primer comprised, in the 5’-3’ direction, a 454-specific adapter, followed by a multiplex identifier (MID, 7bp) and the template-specific primer. The reverse primer included a 454-specific adapter and the template-specific primer. PCR amplification, including number of cycles, was performed as described in Logares et al (2012). Quality control and quantification of PCR products were performed using agarose gels (1.5%, TBE 0.5x). PCR products were purified using the QIAquick® PCR purification Kit (QIAGEN GmbH, Hilden, Germany) and eluted in 45 µl of water (molecular biology grade). Amplicon concentration was estimated using Nanodrop (Thermo Scientific, Wilmington, USA).
  3. 454-pyrosequencing was conducted at the Lund University Sequencing Facility. Two pools of fourteen samples, containing 333.3 ng of DNA each, were produced. In each pool, short fragments were removed using magnetic beads (Agencourt AMPure XP; Beckman Coulter AB, Bromma, Sweden). Pools were subsequently inspected using a DNA 1000 kit on a 2100 Bioanalyzer (Agilent Technologies Sweden AB, Kista, Sweden). Amplicons were quantified using the Quant-iT dsDNA assay kit (Invitrogen) and a Quantiflour fluorometer (Promega Biotech AB, Nacka, Sweden). Pools were diluted to obtain a total of 1×107 copies µL-1. Titration and library production (aiming at 10-15% recovery) were performed using emulsion PCR with the Lib-L kit (Roche AB, Stockholm, Sweden) for unidirectional sequencing. DNA positive beads were enriched, counted on an Innovatis CASY particle counter (Roche), processed using the XLR70 sequencing kit (Roche), and loaded onto a picotiter plate for pyrosequencing on a GS FLX Titanium platform (Roche).

Referencias Bibliográficas

  1. Logares, R., Tesson, S. V., Canbäck, B., Pontarp, M., Hedlund, K., & Rengefors, K. (2018). Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes. Environmental microbiology.

Metadatos Adicionales

Identificadores Alternativos 5f4ccd3e-5b1a-4145-aa43-94ecd45ced8a