virome_antarctic_lakes_2010

Latest version published by SCAR - Microbial Antarctic Resource System on Jun 17, 2021 SCAR - Microbial Antarctic Resource System

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

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How to cite

Researchers should cite this work as follows:

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

Rights

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 9c226382-bbf8-420c-bfcc-bb417be1f181.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Metadata

Contacts

Who created the resource:

Daniel Aguire de Carcer
Universidad Autónoma de Madrid Madrid ES
Alberto Lopez-Bueno
Universidad Autónoma de Madrid Madrid ES
Juan Alonso-Lobo
Universidad Autónoma de Madrid Madrid ES
Antonio Quesada
Universidad Autónoma de Madrid Madrid ES
Antonio Alcami
Universidad Autónoma de Madrid Madrid ES

Who can answer questions about the resource:

Antonio Alcami
Universidad Autónoma de Madrid Madrid ES

Who filled in the metadata:

Maxime Sweetlove
Royal Belgian Institute of Natural Sciences Brussels BE

Who else was associated with the resource:

User
Antonio Alcami
Universidad Autónoma de Madrid Madrid ES

Geographic Coverage

Antarctic Peninsula: Caleta Cierva, Avian Island, Green Island, Pourquoi Pas Island and Livingston Island (South Shetland Islands)

Bounding Coordinates South West [-67.46, -68.54], North East [-62.38, -60.58]

Temporal Coverage

Start Date / End Date 2010-01-21 / 2010-01-28

Project Data

No Description available

Title virome_antarctic_lakes_2010
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)

The personnel involved in the project:

Antonio Alcami

Sampling Methods

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.

Study Extent Samples were taken from several freshwater bodies in the Antarctic Peninsula during the Austral summer 2010.

Method step description:

  1. 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.
  2. 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.
  3. 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).

Bibliographic Citations

  1. 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.

Additional Metadata

Alternative Identifiers https://ipt.biodiversity.aq/resource?r=virome_antarctic_lakes_2010