virome_antarctic_lakes_2010

Daniel Aguire de Carcer1, Alberto Lopez-Bueno1, Juan Alonso-Lobo1, Antonio Quesada1, Antonio Alcami1, Maxime Sweetlove2

1 Universidad Autónoma de Madrid, Madrid, Spain; 2 Royal Belgian Institute of Natural Sciences, Brussels, Belgium

Corresponding author(s): Daniel Aguire de CarcerAlberto Lopez-BuenoJuan Alonso-LoboAntonio QuesadaAntonio Alcami, Maxime Sweetlove (msweetlove@naturalsciences.be)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

de Carcer D A, Lopez-Bueno A, Alonso-Lobo J, Quesada A, Alcami A (2021): virome_antarctic_lakes_2010. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=virome_antarctic_lakes_2010&v=1.0

Abstract

Virome dataset based on shotgun 454 sequencing of virus-concentrated samples from lakes in the Antarctic Peninsula (2010).

Keywords: Metadata

Project details

Project title: virome_antarctic_lakes_2010
Personnel: Antonio Alcami
Funding: "Análisis metagenómico de las comunidades virales de 7 lagos de la Antártida" (Grant ID CTM2009-08644-E, Spanish Polar Programme and the Spanish Ministry of Economy and Competitiviness)

Data published through GBIF: https://ipt.biodiversity.aq/resource?r=virome_antarctic_lakes_2010

Taxonomic coverage

General taxonomic coverage description: Virome, based on shotgun sequencing

Spatial coverage

General spatial coverage: Antarctic Peninsula: Caleta Cierva, Avian Island, Green Island, Pourquoi Pas Island and Livingston Island (South Shetland Islands)
Coordinates: 67°27'36''S and 62°22'48''S Latitude; 68°32'24''W and 60°34'48''W Longitude 

Temporal coverage: January 21, 2010 - January 28, 2010

Methods

Method step description: 
- . 	The filtrated viral fraction was concentrated 100 times by TFF with two cassettes of 70 kDa exclusion size at pressures below 10 p.s.i., in order to maintain viral particle integrity. Viral stocks were preserved at −20°C for transportation, and finally stored at −80°C before subsequent processing. All material was acid-rinsed (0.1 N HCl) and extensively washed with Milli Q or 70 kDa-filtered lake water.
- . 	Frozen stocks were thawed at 4°C with gentle rocking, and then passed through a 25% sucrose cushion by centrifugation for 16 h at 60 000 g and 4°C. The resulting pellets were resuspended in TE buffer (10 mM Tris pH 8, 1 mM EDTA), and filtered using a sterile 0.45 μm syringe filter. Viral concentrates were then treated with DNAse I (500 U ml−1), Nuclease S7 (500 U ml−1), RNAse A (100 μg ml−1) and RNAse H (2 U per reaction) for 30 min at room temperature to remove free nucleic acids. Nuclease reactions were stopped with EDTA and EGTA (12 and 2 mM, respectively), and viral capsids and envelopes were then disrupted with SDS (0.5%) and proteinase K (200 μg ml−1) treatment. 
- . 	Viral DNA was extracted with phenol–chloroform, ethanol precipitated and randomly amplified using Phi29 polymerase and modified random hexamers (GenomiPhi HY, GE Healthcare) for 2.5 h, according to the manufacturer's instructions. The samples were subsequently shot-gun sequenced with a Roche 454 FLX sequencer (Parque Científico de Madrid).
Study extent description: Samples were taken from several freshwater bodies in the Antarctic Peninsula during the Austral summer 2010.

Sampling description: Water samples were preserved at 4°C and viral particles purified within the first 24 h of sampling. From each water body, 60–90 l were first filtered through a 30 μm nylon mesh to remove large particles, and then by tangential flow filtration (TFF) using a peristaltic pump coupled to a Centramate holder (Pall) with two cassettes of 0.45 μm (2 × 0.019 m2, PES) to remove bacteria and smaller eukaryotes. 

Metadata language: English
Date of metadata creation: 2021-06-17
Hierarchy level: Dataset

References
de Cárcer A. D., López-Bueno A., Alonso-Lobo J. M., Quesada A., & Alcamí A. (2016). Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula. FEMS microbiology ecology, 92(6), fiw074.