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Survey of relevant taxonomic groups for the design of qPCR primers and internal fluorescent probes for whole characterization of subaerial biofilm

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A Correction to this article was published on 28 May 2019

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Abstract

Purpose

A deep survey of biodeteriogen microorganisms reported on stone monuments in Europe has been performed based on the available literature dating back to over 30 years.

Methods

The obtained lists for eukaryotic algae, phototrophic and non-phototrophic bacteria, and fungi were sorted by Genera, and corresponding sequences in triplicate were downloaded by nucleotide database Genbank for a number of selected barcoding markers. On the basis of collected bibliometric diversity, multiple nucleotide alignments were produced and primers were designed for a qPCR assay. The aim of the present study was to obtain accurate oligos for the characterization of subaerial biofilms on the basis of the most comprehensive collection of reports and case studies regarding subaerial biofilms, with particular regard to phototrophic and non-phototrophic bacteria, eukaryotic algae, and molds.

Result

Primers were designed on conserved regions flanking a variable region, specific for each of the studied groups of microorganisms. Standard curve for absolute quantification relative to each group were determined for four markers. Then, variable regions in the alignments were used to design fluorescent internal probes for qPCR aimed for a multiplex reaction in which relative abundance can be determined.

Conclusion

The authors propose this kind of cost-effective approach in the study of biofilms for the estimation of algae, molds, and bacteria both for direct in situ analysis and in vitro simulation.

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Change history

  • 28 May 2019

    The term ‘subaerial biofilm’ (SAB) has been introduced for microbial communities that develop on solid mineral surfaces exposed to the atmosphere.

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Authors and Affiliations

  1. Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126, Naples, Italy

    Angelo Del Mondo, Antonino De Natale, Gabriele Pinto & Antonino Pollio

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  1. Angelo Del Mondo
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  2. Antonino De Natale
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  3. Gabriele Pinto
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  4. Antonino Pollio
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Correspondence to Angelo Del Mondo.

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Del Mondo, A., De Natale, A., Pinto, G. et al. Survey of relevant taxonomic groups for the design of qPCR primers and internal fluorescent probes for whole characterization of subaerial biofilm. Ann Microbiol 69, 1087–1096 (2019). https://doi.org/10.1007/s13213-019-01461-y

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