Bacterial Diversity Assessment in Antarctic Terrestrial and Aquatic Microbial Mats

Versão mais recente published by SCAR - Microbial Antarctic Resource System on mar 19, 2019 SCAR - Microbial Antarctic Resource System
Publication date:
19 de Março de 2019
Licença:
CC-BY 4.0

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Descrição

Bacterial data (16S rRNA) from terrestrial and aquatic Microbial mats in continental Antarctic.

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

Tytgat B, Vrleyen E, Obbels D, Peeters K, De Wever A, D'hondt S, De Meyer T, van Criekinge W, Vyverman W, Willems A (2018): Bacterial Diversity Assessment in Antarctic Terrestrial and Aquatic Microbial Mats. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacterial_diversity_antarctica_microbial_mats&v=1.1

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: f3a8b1d6-a1d1-4292-8a7e-19c63a0825bd.  SCAR - Microbial Antarctic Resource System publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por Scientific Committee on Antarctic Research.

Palavras-chave

lake; soil; bacteria; antarctica; 16S

Contatos

Bjorn Tytgat
  • Provedor De Conteúdo
  • Originador
  • Ponto De Contato
Post doctoral assistent
Ghent University
Krijgslaan 281
9000 Gent
BE
Elie Vrleyen
  • Originador
Professor
Ghent University
Krijgslaan 281
9000 Gent
BE
Dagmar Obbels
  • Originador
PhD student
Ghent University
Krijgslaan 281
9000 Gent
BE
Karolien Peeters
  • Provedor De Conteúdo
  • Originador
Post doctoral researcher
Ghent University
Krijgslaan 281
9000 Gent
BE
Aake De Wever
  • Originador
Post doctoral assistent
Royal Belgian Institute for Natural Sciences
Krijgslaan 281
1000 Brussels
BE
Sofie D'hondt
  • Originador
Lab technician
Ghent University
Tim De Meyer
  • Originador
Professor
Ghent University
Wim van Criekinge
  • Originador
Post doctoral researcher
GhentUniversity
Wim Vyverman
  • Originador
Professor
Ghent University
Anne Willems
  • Provedor De Conteúdo
  • Originador
Professor
Ghent Univeristy
Maxime Sweetlove
  • Provedor Dos Metadados
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
1000 Brussels
BE

Cobertura Geográfica

soil samples and lake samples from East Antarctica

Coordenadas delimitadoras Sul Oeste [-80,45, -67,45], Norte Leste [-67,7, 39,8]

Cobertura Taxonômica

Bacterial 16S amplicons (V1-V3 region)

Domínio Bacteria (Bacteria)

Cobertura Temporal

Data Inicial / Data final 2003-01-01 / 2007-01-01

Dados Sobre o Projeto

CCAMBIO (Climate Change and Antarctic Microbial Biodiversity) is an academic project funded by the Belgian Federal Science Policy (BELSPO). Its main objective is to study the diversity, biogeographic zoning and genomic make-up of lacustrine microbial mat communities in the Antarctic Realm. CCAMBIO is composed by researchers from four Belgian Universities and Institutes (University of Liège, Ghent University, National Botanical Garden of Belgium and Royal Belgian Institute of Natural Sciences), as well as collaborators from the British Antarctic Survey.

Título CCAMBIO
Identificador CCAMBIO
Financiamento Belgian Science Policy Office (BelSPO) project SD/BA/03

O pessoal envolvido no projeto:

Bjorn Tytgat
Elie Verleyen
Dagmar Obbels
Anne Willems
Wim Vyverman

Métodos de Amostragem

Two terrestrial and seven limnetic microbial mat samples were collected aseptically during different field campaigns in December/January 2003 (PQ1, TM2 and TM4) and in January 2007 (BB50, BB115, LA3, SK5, WO10 and SO6). All samples were kept frozen during transport and stored at 220uC.

Área de Estudo One sample (PQ1) was collected on Pourquoi-Pas Island off the west coast of Graham Land (Antarctic Peninsula). All other samples were collected from Eastern Antarctic habitats. The two terrestrial microbial mat samples (BB50 and BB115) were taken near the Utsteinen nunatak in the Sør Rondane Mountains (Dronning Maud Land). Three samples were from Lu ̈tzow-Holm Bay (Dronning Maud Land), namely from a small saline lake in Langhovde (LA3), from Naka-Tempyo Lake (SK5) in Skarvsnes, and from a small saline pond (WO10) in West Ongul Island. One sample (SO6) was taken from Lake Melkoye (unofficial name) in Schirmacher Oasis (Dronning Maud Land). The two remaining samples were collected in the Transantarctic Mountains. Sample TM2 was taken from Forlidas Pond (Dufek Massif, Pensacola Mountains), while sample TM4 was taken from Lundstro ̈m Lake (Shackleton Range).

Descrição dos passos do método:

  1. DNA was extracted from frozen samples using 5 g per sample. Extracellular DNA was first removed as described by Corinaldesi et al. and DNA extraction was subsequently performed according to Zwart et al. Sequencing of the 16S rRNA V1–V3 regions was performed using forward primer pA (AGAGTTTGATCCTGGCTCAG 8–27) and reverse primer BKL1 (GTATTACCGCGGCTGCTGGCA 536– 516). Because it proved impossible to concatenate the comple- mentary reads due to insufficient overlap, the forward and reverse sequences were analyzed separately. The forward reads hence cover the complete V1 and V2 regions, whereas the reverse reads cover the V3 and part of the V2 region for the longest sequences.
  2. Multiplexing was done with barcodes proposed by Parames- waran et al. Each PCR mixture contained 1–2 ml of template DNA, 2 ml of fusion primers and barcodes (10 mM), 2.5 ml dNTPs (10 mM), 1.5 ml of 10x buffer, 0.25 ml of 5 U/ml FastStart High Fidelity Polymerase (Roche) and was adjusted to a final volume of 25 ml with sterile HPLC-water. PCR cycling included 3 min at 94uC, followed by 35 cycles of 94uC for 30 s, 55uC for 60 s and 72uC for 90 s and finally 8 min at 72uC. PCR products were purified using a High Pure PCR Product Purification Kit (Roche).
  3. Pyrosequencing was performed on a Roche 454 GS FLX Titanium machine at NXTGNT (Ghent, Belgium) after quality control of the DNA with a Qubit 2.0 Fluorometer (Life Technologies) and a Bioanalyzer (Agilent Technologies).

Citações bibliográficas

  1. Tytgat, B., Verleyen, E., Obbels, D., Peeters, K., De Wever, A., D’hondt, S., ... & Willems, A. (2014). Bacterial diversity assessment in Antarctic terrestrial and aquatic microbial mats: a comparison between bidirectional pyrosequencing and cultivation. PloS one, 9(6), e97564.

Metadados Adicionais

Identificadores alternativos f3a8b1d6-a1d1-4292-8a7e-19c63a0825bd
https://ipt.biodiversity.aq/resource?r=bacterial_diversity_antarctica_microbial_mats