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In-depth Characterization via Complementing Culture-Independent Approaches of the Microbial Community in an Acidic Hot Spring of the Colombian Andes

  • Environmental Microbiology
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An Erratum to this article was published on 12 November 2011

Abstract

The microbial community of a Colombian high mountain hot spring, El Coquito, was analyzed using three different culture-independent assessments of 16S ribosomal RNA genes: clone libraries, pyrosequencing of the V5–V6 hypervariable region, and microarray. This acidic spring had a diverse community composed mainly of Bacteria that shared characteristics with those from other hot springs and extreme acidic environments. The microbial community was dominated by Proteobacteria, Firmicutes, and Planctomycetes and contained chemotrophic bacteria potentially involved in cycling of ferrous and sulfur-containing minerals and phototrophic organisms, most of which were eukaryotic micro-algae. Despite the presence of a large proportion of novel, unclassified sequences, the taxonomic profiles obtained with each strategy showed similarities at higher taxonomic levels. However, some groups, such as Spirochaetes and Aquificae, were identified using only one methodology, and more taxa were detected with the gene array, which also shared more groups with the pyrosequencing data. Overall, the combined use of different approaches provided a broader view of the microbial community in this acidic hot spring.

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Acknowledgments

We would like to thank to José Ricardo Bustos, Luis Miguel Rodríguez and Silvia Restrepo for technical assistance with setting up local server installations of bioinformatics programs, Luis Miguel Alvarez for sampling, Jose Salvador Montaña for sampling and processing DNA, and Yvette Piceno, Eoin Brodie and Gary Andersen for providing us access to the PhyloChip. This work was financed by Colciencias—SENA (project no. 6570-392-19990) and was done under MAVDT contract no. 15, 2008 for access to genetic resources and UAESPNN Research permit no. DTNO-N-20/2007.

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  1. Vanja Klepac-Ceraj

    Present address: The Forsyth Institute, 245 First Street, Cambridge, MA, 02142, USA

Authors and Affiliations

  1. Molecular Genetics & Biotechnology, Corporación CorpoGen, Carrera 5 No. 66A-34, 110231, Bogotá, DC, Colombia

    Laura C. Bohorquez, Luisa Delgado-Serrano, César Osorio-Forero, Howard Junca & María Mercedes Zambrano

  2. Colombian Center for Genomics and Bioinformatics of Extreme Environments—GeBiX, Carrera 5 No. 66A-34, 110231, Bogotá, DC, Colombia

    Laura C. Bohorquez, Luisa Delgado-Serrano, Gina López, César Osorio-Forero, Howard Junca, Sandra Baena & María Mercedes Zambrano

  3. Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, PO Box 56710, Bogotá, DC, Colombia

    Gina López & Sandra Baena

  4. Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA

    Vanja Klepac-Ceraj & Roberto Kolter

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Additional information

An erratum to this article can be found at http://dx.doi.org/10.1007/s00248-011-9977-6

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Supplementary Table 1

Abundance of taxa from phylum to order for the three methods used. The number of OTUs is shown for Phylochip, the number of total sequences for 454 pyrotags, and the number of sequences for each separate clone library (Bacteria and Archaea). Abundance was determined as the percentage of the total for each strategy. In bold are the subtotals for each group (DOC 170 kb)

Supplementary Figure 1

Phylogenetic reconstruction of sequences from El Coquito hot spring. Green branches indicate unique sequences obtained by Phylochip, dark blue branches indicate unique sequences obtained by 454 pyrotags, light blue indicates unclassified sequences of 454 pyrotags, red branches indicate unique sequences obtained by clone libraries, and black branches indicate reference sequences. The asterisk indicates a novel deepbranching cluster. The scale bar shows the distance of 0.08 nucleotides substitutions per hundred nucleotides (PDF 252 kb)

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Bohorquez, L.C., Delgado-Serrano, L., López, G. et al. In-depth Characterization via Complementing Culture-Independent Approaches of the Microbial Community in an Acidic Hot Spring of the Colombian Andes. Microb Ecol 63, 103–115 (2012). https://doi.org/10.1007/s00248-011-9943-3

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