Detection and Quantification of Nitrifying Bacteria Using Real-Time PCR

Engil I P Pereira; Marcelo C M Teixeira Filho

doi:10.1007/978-1-4939-9790-9_13

Detection and Quantification of Nitrifying Bacteria Using Real-Time PCR

Methods Mol Biol. 2020:2057:145-153. doi: 10.1007/978-1-4939-9790-9_13.

Authors

Engil I P Pereira¹, Marcelo C M Teixeira Filho²

Affiliations

¹ School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, USA.
² Department of Plant Protection, Rural Engineering and Soils, São Paulo State University (UNESP), Ilha Solteira, SP, Brazil. mcmtf@yahoo.com.br.

PMID: 31595477
DOI: 10.1007/978-1-4939-9790-9_13

Abstract

Nitrification is the microbial-mediated transformation of ammonium (NH₄⁺) into nitrate (NO₃^-). Many plant species depend on the availability of NO₃^- as the main source of nitrogen (N). On the other hand, because NO₃^- is highly mobile in the soil profile, its excess concentration can cause environmental pollution. Nitrification can be estimated at the process level, but with the development of molecular techniques it is also possible to estimate the abundance of nitrifying bacteria in the soil. Hence, in this chapter we describe the procedure for detection and quantification of nitrifying bacteria in soil samples using real-time quantitative polymerase chain reaction (PCR).

Keywords: Amplification efficiency; DNA extraction; Nitrification; Nitrifying gene; Nitrosomonas europaea.

MeSH terms

Bacteria / genetics
Bacteria / isolation & purification*
Bacteria / metabolism*
DNA, Bacterial / isolation & purification
Nitrification*
Nitrosomonas europaea / genetics
Nitrosomonas europaea / metabolism
Real-Time Polymerase Chain Reaction / methods*
Soil Microbiology
Workflow

Substances

DNA, Bacterial