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An oligonucleotide prokaryotic acidophile microarray: its validation and its use to monitor seasonal variations in extreme acidic environments with total environmental RNA

Authors

  • Patricia Garrido,

    1. Centro de Astrobiología (CSIC-INTA), carretera de Ajalvir km 4, 28850, Torrejón de Ardoz, Madrid, Spain.
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    • Present address: Genetrix S.L. Calle Marconi, 1. Parque Tecnológico de Madrid, 28760 Tres Cantos, Madrid, Spain.

  • Elena González-Toril,

    1. Centro de Astrobiología (CSIC-INTA), carretera de Ajalvir km 4, 28850, Torrejón de Ardoz, Madrid, Spain.
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  • Antonio García-Moyano,

    1. Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain.
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  • Mercedes Moreno-Paz,

    1. Centro de Astrobiología (CSIC-INTA), carretera de Ajalvir km 4, 28850, Torrejón de Ardoz, Madrid, Spain.
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  • Ricardo Amils,

    1. Centro de Astrobiología (CSIC-INTA), carretera de Ajalvir km 4, 28850, Torrejón de Ardoz, Madrid, Spain.
    2. Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain.
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  • Víctor Parro

    Corresponding author
    1. Centro de Astrobiología (CSIC-INTA), carretera de Ajalvir km 4, 28850, Torrejón de Ardoz, Madrid, Spain.
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*E-mail parrogv@inta.es; Tel. (+34) 915201071; Fax (+34) 915201074.

Summary

An oligonucleotide microarray that monitors prokaryotic diversity in extremely acidic environments has been developed. The oligonucleotide probes target most known acidophilic microorganisms, including members of the Nitrospira phylum, Acidithiobacillus genus, acidobacteria, sulfur reducing bacteria, Actinobacteria and Archaea of the Ferroplasma and Thermoplasma genera. The probes were tested for their specificity against the corresponding type strain by microarray hybridization using PCR-amplified fluorescent DNA of the 16S rRNA genes. The microarray was tested and validated against well-established molecular ecology techniques such as molecular cloning and sequencing and FISH by using samples obtained from a natural extremely acidic environment, the Río Tinto (SW Spain). Also, fluorescent labelled total environmental RNA from Río Tinto samples were used as targets for microarray hybridizations. This approach allowed the detection of the most metabolically active prokaryotes of the ecosystem by simultaneously checking probes against 16S and 23S rRNAs as well as other functional genes. Seasonal and spatial variations in the relative expression of specific rRNA genes have been detected between two sampling sites that differ in several physicochemical parameters, mainly iron and sulfur content.

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