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

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

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). New York: 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