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Quantification of Ammonia Oxidizing Bacterial Abundances in Environmental Samples by Quantitative-PCR

Blaud, Aimeric; Ma�der, Abadie; Clark, Ian M.

Authors

Abadie Ma�der

Ian M. Clark



Contributors

Lilia C. Carvalhais
Editor

Paul G. Dennis
Editor

Abstract

Quantitative-PCR (qPCR) enables the quantification of specific DNA targets, such as functional or phylogenetic marker genes associated with environmental samples. During each qPCR cycle, the number of copies of a gene (or region) of interest in DNA samples is determined in real time using a fluorescence-based label and compared to a standard serial dilution. Here, we describe a qPCR method to quantify the ammonia oxidizing bacteria involved in the first step of nitrification, using the amoA gene as a proxy of their abundance. The preparation of the standards from environmental samples and qPCR is presented in detail for specifically quantifying microbial abundance in environmental samples such as soil.

Citation

Blaud, A., Maïder, A., & Clark, I. M. (2021). Quantification of Ammonia Oxidizing Bacterial Abundances in Environmental Samples by Quantitative-PCR. In L. C. Carvalhais, & P. G. Dennis (Eds.), The Plant Microbiome: Methods and Protocols (135-146). Springer. https://doi.org/10.1007/978-1-0716-1040-4_12

Online Publication Date Nov 8, 2020
Publication Date 2021
Deposit Date Aug 24, 2021
Publisher Springer
Pages 135-146
Series Title Methods in Molecular Biology
Series Number 2232
Series ISSN 1064-3745
Book Title The Plant Microbiome: Methods and Protocols
ISBN 978-1-0716-1039-8
DOI https://doi.org/10.1007/978-1-0716-1040-4_12
Keywords qPCR, PCR, Standard curve, Melting curve, Gel extraction, SYBR Green, Ammonia-oxidizing bacteria, amoA
Public URL http://researchrepository.napier.ac.uk/Output/2795221