Quantification of Complete Ammonia Oxidizing (Comammox) Bacteria Clades and Strict Nitrite Oxidizers in Nitrospira Using Newly Designed Primers.

Quantification of Complete Ammonia Oxidizing (Comammox) Bacteria Clades and Strict Nitrite Oxidizers in Nitrospira Using Newly Designed Primers. Appl Environ Microbiol. 2020 Aug 21;: Authors: Jiang R, Wang JG, Zhu T, Zou B, Wang DQ, Rhee SK, An D, Ji ZY, Quan ZX Abstract Complete ammonia oxidizing (comammox) bacteria play key roles in environmental nitrogen cycling and all belong to the genus Nitrospira, which was originally believed to include only strict nitrite-oxidizing bacteria (sNOB). Thus, differential estimation of sNOB abundance from comammox Nitrospira has become problematic since both contain nitrite oxidoreductase genes that serve as common targets for sNOB detection. Herein, we developed novel comammox Nitrospira clades A- and B-specific primer sets targeting the α-subunit of ammonia monooxygenase gene (amoA) and a sNOB-specific primer set targeting cyanase gene (cynS) for quantitative PCR (qPCR). The high coverage and specificity of these primers had been checked by metagenome and metatranscriptome datasets. Efficient and specific amplification with these primers were demonstrated using various environmental samples. Using the newly designed primers, we successfully estimated the abundances of comammox Nitrospira and sNOB in samples from two chloramination-treated drinking water systems and found that, in most samples, comammox Nitrospira clade A was the dominant Nitrospira, and also served as the primary ammonia oxidi...
Source: Applied and Environmental Microbiology - Category: Microbiology Authors: Tags: Appl Environ Microbiol Source Type: research