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Evaluation of the Abundance of Fungi in Wastewater Treatment Plants Using Quantitative PCR (qPCR)

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Quantitative Real-Time PCR

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2065))

Abstract

Assessment of the abundance of fungi in environmental samples by quantitative PCR (qPCR) of community DNA is often a difficult task due to biases introduced during PCR amplification, resulting from the differences associated with length polymorphism and the varying number of copies of the rRNA operon among fungal species, the lack of specificity of the primers targeting the different regions of the rRNA operon, or their insufficient coverage of the fungal lineages. To overcome those limitations, it is crucial to test and select the specific primers sets which provide the more accurate approximation to the quantification of the targeted fungal populations in a given set of samples. Fungi are a significant fraction of the microbiota in wastewater treatment plants (WWTPs), but the activated sludge microbial communities comprise many other eukaryotic microorganisms whose molecular markers are often coamplified by primers initially designed as fungal-specific. Here, the use of the FungiQuant primer set is recommended for the quantification of fungal molecular markers (18S rRNA genes) by qPCR in activated sludge samples and the full protocol is described.

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Acknowledgments

This work was supported by Junta de Andalucía, Plan Andaluz de Investigación (Environmental Microbiology Group, RNM-270).

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Authors and Affiliations

  1. Department of Microbiology, Institute of Water Research, University of Granada, Granada, Spain

    Paula Maza-Márquez, Elisabet Aranda, Jesús González-López & Belén Rodelas

  2. Environmental Microbiology Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain

    Paula Maza-Márquez

Authors
  1. Paula Maza-Márquez
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  2. Elisabet Aranda
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  3. Jesús González-López
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  4. Belén Rodelas
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Corresponding author

Correspondence to Paula Maza-Márquez .

Editor information

Editors and Affiliations

  1. Molecular Diagnostics, IRCCS, Istituto Giannina Gaslini, Genova, Italy

    Roberto Biassoni

  2. ASL3 Sistema Sanitario Regione Liguria, S.C. Laboratorio d’Analisi, Genova, Italy

    Alessandro Raso

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Maza-Márquez, P., Aranda, E., González-López, J., Rodelas, B. (2020). Evaluation of the Abundance of Fungi in Wastewater Treatment Plants Using Quantitative PCR (qPCR). In: Biassoni, R., Raso, A. (eds) Quantitative Real-Time PCR. Methods in Molecular Biology, vol 2065. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9833-3_7

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  • DOI: https://doi.org/10.1007/978-1-4939-9833-3_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9832-6

  • Online ISBN: 978-1-4939-9833-3

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