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Microbiomes of Biofilms on Decorative Siliceous Stone: Drawbacks and Advantages of Next Generation Sequencing

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Abstract

Next Generation Sequencing (NGS), using the Illumina® metabarcoding system, showed differences between biofilm communities on three degraded siliceous stone church façades in central Rio de Janeiro. Two church biofilms (on granite and augen gneiss) were dominated by Actinobacteria; the third (granite), surrounded by trees and further from intense vehicular traffic, by Gammaproteobacteria. Yeast-like forms of Basidiomycetes and Ascomycetes were major fungi on all facades, but 22.8% of Operational Taxonomic Units could not be assigned to any fungal taxon after DNA amplification with ITS primers and analysis with the UNITE database, indicating the need for more fungal NGS studies. The pipeline used in analysis of the V4 region of rRNA bacterial gene sequences influenced the taxa detected, with two major classes and many genera identified only by the pipeline using the Greengenes, and not the Silva, database. Principal Components Analysis separated façade biofilms into the appropriate three groups and indicated greater dissimilarity of the tree-surrounded church biofilm from the others, confirmed by Jaccard Similarity coefficients, suggesting that local environment influences community composition more than stone type. NGS allows rapid and detailed analysis of microbiomes, but results must be carefully assessed and must not be used as the sole indication of community composition.

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Authors and Affiliations

  1. Department Microbiology and Plant Biology, University of Oklahoma, Norman, USA

    Akiko Ogawa, Sukriye Celikkol-Aydin, Christine Gaylarde & Iwona Beech

  2. Department Chemistry and Biochemistry, Suzuka College, National Institute of Technology, Suzuka, Japan

    Akiko Ogawa

  3. Department Geology, Universidade Federal Fluminense, Niterói, Brazil

    Jose Antônio Baptista-Neto

Authors
  1. Akiko Ogawa
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  2. Sukriye Celikkol-Aydin
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  3. Christine Gaylarde
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  4. Jose Antônio Baptista-Neto
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  5. Iwona Beech
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Correspondence to Christine Gaylarde.

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Ogawa, A., Celikkol-Aydin, S., Gaylarde, C. et al. Microbiomes of Biofilms on Decorative Siliceous Stone: Drawbacks and Advantages of Next Generation Sequencing. Curr Microbiol 74, 848–853 (2017). https://doi.org/10.1007/s00284-017-1257-3

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  • DOI: https://doi.org/10.1007/s00284-017-1257-3

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